Sample records for gen agxt r197q

  1. Identification of 5 novel mutations in the AGXT gene.

    PubMed

    Basmaison, O; Rolland, M O; Cochat, P; Bozon, D

    2000-06-01

    In order to identify additional genotypes in primary hyperoxaluria type 1, we sequenced the AGXT genes of 9 patients. We report 5 new mutations. Three are splice-site mutations situated at the end of intron 4 and 8 (647-1G>A, 969-1G>C, 969-3C>G), one is a missense mutation in exon 5 (D183N), and one is a short duplication in exon 2 (349ins7). Their consequence is always a lack of enzymatic activity of the Alanine-Glyoxylate Aminotransferase (AGT); for 4 of them, we were able to deduce that they were associated to the absence of AGT protein. These mutations are rare, as they have been found on one allele in our study (except 969-3C>G present in 2 unrelated families), and have not been previously reported. PMID:10862087

  2. Alanine-glyoxylate aminotransferase 2 (AGXT2) polymorphisms have considerable impact on methylarginine and ?-aminoisobutyrate metabolism in healthy volunteers.

    PubMed

    Kittel, Anja; Müller, Fabian; König, Jörg; Mieth, Maren; Sticht, Heinrich; Zolk, Oliver; Kralj, Ana; Heinrich, Markus R; Fromm, Martin F; Maas, Renke

    2014-01-01

    Elevated plasma concentrations of asymmetric (ADMA) and symmetric (SDMA) dimethylarginine have repeatedly been linked to adverse clinical outcomes. Both methylarginines are substrates of alanine-glyoxylate aminotransferase 2 (AGXT2). It was the aim of the present study to simultaneously investigate the functional relevance and relative contributions of common AGXT2 single nucleotide polymorphisms (SNPs) to plasma and urinary concentrations of methylarginines as well as ?-aminoisobutyrate (BAIB), a prototypic substrate of AGXT2. In a cohort of 400 healthy volunteers ADMA, SDMA and BAIB concentrations were determined in plasma and urine using HPLC-MS/MS and were related to the coding AGXT2 SNPs rs37369 (p.Val140Ile) and rs16899974 (p.Val498Leu). Volunteers heterozygous or homozygous for the AGXT2 SNP rs37369 had higher SDMA plasma concentrations by 5% and 20% (p?=?0.002) as well as higher BAIB concentrations by 54% and 146%, respectively, in plasma and 237% and 1661%, respectively, in urine (both p<0.001). ADMA concentrations were not affected by both SNPs. A haplotype analysis revealed that the second investigated AGXT2 SNP rs16899974, which was not significantly linked to the other AGXT2 SNP, further aggravates the effect of rs37369 with respect to BAIB concentrations in plasma and urine. To investigate the impact of the amino acid exchange p.Val140Ile, we established human embryonic kidney cell lines stably overexpressing wild-type or mutant (p.Val140Ile) AGXT2 protein and assessed enzyme activity using BAIB and stable-isotope labeled [²H?]-SDMA as substrate. In vitro, the amino acid exchange of the mutant protein resulted in a significantly lower enzyme activity compared to wild-type AGXT2 (p<0.05). In silico modeling of the SNPs indicated reduced enzyme stability and substrate binding. In conclusion, SNPs of AGXT2 affect plasma as well as urinary BAIB and SDMA concentrations linking methylarginine metabolism to the common genetic trait of hyper-?-aminoisobutyric aciduria. PMID:24586340

  3. Alanine-glyoxylate aminotransferase 2 (AGXT2) Polymorphisms Have Considerable Impact on Methylarginine and ?-aminoisobutyrate Metabolism in Healthy Volunteers

    PubMed Central

    König, Jörg; Mieth, Maren; Sticht, Heinrich; Zolk, Oliver; Kralj, Ana; Heinrich, Markus R.; Fromm, Martin F.; Maas, Renke

    2014-01-01

    Elevated plasma concentrations of asymmetric (ADMA) and symmetric (SDMA) dimethylarginine have repeatedly been linked to adverse clinical outcomes. Both methylarginines are substrates of alanine-glyoxylate aminotransferase 2 (AGXT2). It was the aim of the present study to simultaneously investigate the functional relevance and relative contributions of common AGXT2 single nucleotide polymorphisms (SNPs) to plasma and urinary concentrations of methylarginines as well as ?-aminoisobutyrate (BAIB), a prototypic substrate of AGXT2. In a cohort of 400 healthy volunteers ADMA, SDMA and BAIB concentrations were determined in plasma and urine using HPLC-MS/MS and were related to the coding AGXT2 SNPs rs37369 (p.Val140Ile) and rs16899974 (p.Val498Leu). Volunteers heterozygous or homozygous for the AGXT2 SNP rs37369 had higher SDMA plasma concentrations by 5% and 20% (p?=?0.002) as well as higher BAIB concentrations by 54% and 146%, respectively, in plasma and 237% and 1661%, respectively, in urine (both p<0.001). ADMA concentrations were not affected by both SNPs. A haplotype analysis revealed that the second investigated AGXT2 SNP rs16899974, which was not significantly linked to the other AGXT2 SNP, further aggravates the effect of rs37369 with respect to BAIB concentrations in plasma and urine. To investigate the impact of the amino acid exchange p.Val140Ile, we established human embryonic kidney cell lines stably overexpressing wild-type or mutant (p.Val140Ile) AGXT2 protein and assessed enzyme activity using BAIB and stable-isotope labeled [2H6]-SDMA as substrate. In vitro, the amino acid exchange of the mutant protein resulted in a significantly lower enzyme activity compared to wild-type AGXT2 (p<0.05). In silico modeling of the SNPs indicated reduced enzyme stability and substrate binding. In conclusion, SNPs of AGXT2 affect plasma as well as urinary BAIB and SDMA concentrations linking methylarginine metabolism to the common genetic trait of hyper-?-aminoisobutyric aciduria. PMID:24586340

  4. Partial deletion of the AGXT gene (EX1_EX7del): A new genotype in hyperoxaluria type 1.

    PubMed

    Nogueira, P K; Vuong, T S; Bouton, O; Maillard, A; Marchand, M; Rolland, M O; Cochat, P; Bozon, D

    2000-04-01

    Primary hyperoxaluria type 1 (PH1) is a rare autosomal (2q37.3) recessive metabolic disease caused by a deficiency of the hepatic peroxisomal enzyme alanine:glyoxylate amino transferase. Molecular heterogeneity is important in PH1 as most of the patients (if the parents are unrelated) are compound heterozygotes for rare mutations. We describe the first large deletion in the AGXT gene, removing exons 1 to 7 (EX1_EX7del) that was responsible for one case of severe PH1. This 10 kb deletion was identified by Southern blotting of genomic DNA digested by Xba I and hybridized with different exonic probes. Both parents (from Turkey) are first cousin and carry the deletion. It is of note that the presently reported patient did not exhibit any AGT catalytic activity and even so, he progressed towards end-stage renal disease only at 19 years old. PMID:10737993

  5. GenBank

    PubMed Central

    Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Rapp, Barbara A.; Wheeler, David L.

    2000-01-01

    The GenBank® sequence database incorporates publicly available DNA sequences of >55 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (Web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI’s integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping and protein structure information, plus the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of WWW retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov PMID:10592170

  6. GenBank.

    PubMed

    Benson, Dennis A; Cavanaugh, Mark; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

    2013-01-01

    GenBank® (http://www.ncbi.nlm.nih.gov) is a comprehensive database that contains publicly available nucleotide sequences for almost 260 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov. PMID:23193287

  7. GenBank.

    PubMed

    Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

    2008-01-01

    GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov. PMID:18073190

  8. GenBank.

    PubMed

    Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

    2010-01-01

    GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov. PMID:19910366

  9. GenBank.

    PubMed

    Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

    2011-01-01

    GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov. PMID:21071399

  10. GenBank.

    PubMed

    Benson, Dennis A; Karsch-Mizrachi, Ilene; Clark, Karen; Lipman, David J; Ostell, James; Sayers, Eric W

    2012-01-01

    GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 250,00 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov. PMID:22144687

  11. GenBank.

    PubMed

    Benson, Dennis A; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

    2014-01-01

    GenBank is a comprehensive database that contains publicly available nucleotide sequences for over 280,000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov. PMID:24217914

  12. GenBank.

    PubMed

    Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

    2009-01-01

    GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank(R) staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov. PMID:18940867

  13. GenBank

    PubMed Central

    Benson, Dennis A.; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Sayers, Eric W.

    2015-01-01

    GenBank® (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. PMID:25414350

  14. GenBank.

    PubMed

    Benson, Dennis A; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

    2015-01-01

    GenBank(®) (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. PMID:25414350

  15. Gen IV LFR \\

    Microsoft Academic Search

    N. Li; J. S. Zhang; H. D. Yu; J. Jansen

    This report presents the status of the model-based analysis of the publicly reported corrosion test data and use of the model to extract long term corrosion rates, a main analytical task of the LANL's Gen IV LFR Work Package \\

  16. Verifying Test Hypotheses -HOL/TestGen Verifying Test Hypotheses -HOL/TestGen

    E-print Network

    Verifying Test Hypotheses - HOL/TestGen Verifying Test Hypotheses - HOL/TestGen An Experiment in Test and Proof Thomas Malcher January 20, 2014 1 / 20 #12;Verifying Test Hypotheses - HOL/TestGen HOL/TestGen Outline Introduction Test Hypotheses HOL/TestGen - Demo Verifying Test Hypotheses Conclusion 2 / 20 #12

  17. FutureGen Project Report

    SciTech Connect

    Cabe, Jim; Elliott, Mike

    2010-09-30

    This report summarizes the comprehensive siting, permitting, engineering, design, and costing activities completed by the FutureGen Industrial Alliance, the Department of Energy, and associated supporting subcontractors to develop a first of a kind near zero emissions integrated gasification combined cycle power plant and carbon capture and storage project (IGCC-CCS). With the goal to design, build, and reliably operate the first IGCC-CCS facility, FutureGen would have been the lowest emitting pulverized coal power plant in the world, while providing a timely and relevant basis for coal combustion power plants deploying carbon capture in the future. The content of this report summarizes key findings and results of applicable project evaluations; modeling, design, and engineering assessments; cost estimate reports; and schedule and risk mitigation from initiation of the FutureGen project through final flow sheet analyses including capital and operating reports completed under DOE award DE-FE0000587. This project report necessarily builds upon previously completed siting, design, and development work executed under DOE award DE-FC26- 06NT4207 which included the siting process; environmental permitting, compliance, and mitigation under the National Environmental Policy Act; and development of conceptual and design basis documentation for the FutureGen plant. For completeness, the report includes as attachments the siting and design basis documents, as well as the source documentation for the following: • Site evaluation and selection process and environmental characterization • Underground Injection Control (UIC) Permit Application including well design and subsurface modeling • FutureGen IGCC-CCS Design Basis Document • Process evaluations and technology selection via Illinois Clean Coal Review Board Technical Report • Process flow diagrams and heat/material balance for slurry-fed gasifier configuration • Process flow diagrams and heat/material balance for dry-fed gasifier configuration • Full capital cost report and cost category analysis (CAPEX) • Full operating cost report and assumptions (OPEX) Comparative technology evaluations, value engineering exercises, and initial air permitting activities are also provided; the report concludes with schedule, risk, and cost mitigation activities as well as lessons learned such that the products of this report can be used to support future investments in utility scale gasification and carbon capture and sequestration. Collectively, the FutureGen project enabled the comprehensive site specific evaluation and determination of the economic viability of IGCC-CCS. The project report is bound at that determination when DOE formally proposed the FutureGen 2.0 project which focuses on repowering a pulverized coal power plant with oxy-combustion technology including CCS.

  18. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend.

    PubMed

    Stackebrandt, E; Koch, C; Gvozdiak, O; Schumann, P

    1995-10-01

    The results of a phylogenetic and chemotaxonomic analysis of the genus Micrococcus indicated that it is significantly heterogeneous. Except for Micrococcus lylae, no species groups phylogenetically with the type species of the genus, Micrococcus luteus. The other members of the genus form three separate phylogenetic lines which on the basis of chemotaxonomic properties can be assigned to four genera. These genera are the genus Kocuria gen. nov. for Micrococcus roseus, Micrococcus varians, and Micrococcus kristinae, described as Kocuria rosea comb. nov., Kocuria varians comb. nov., and Kocuria kristinae comb. nov., respectively; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Dermacoccus gen. nov. for Micrococcus nishinomiyaensis, described as Dermacoccus nishinomiyaensis comb. nov.; and the genus Kytocossus gen. nov. for Micrococcus sedentarius, described as Kytococcus sedentarius comb. nov. M. luteus and M. lylae, which are closely related phylogenetically but differ in some chemotaxonomic properties, are the only species that remain in the genus Micrococcus Cohn 1872. An emended description of the genus Micrococcus is given [corrected]. PMID:7547287

  19. OPUS SQL GEN Shaw-Hong Kao

    E-print Network

    Sirianni, Marco

    OPUS SQL GEN Shaw-Hong Kao November 27, 1996 Usage To generate load opus sql output le, at command line, type : $ opus_sql_gen p1] where p1 = delivery number, if ommit, use default delivery_number.value It will create output le opus .sql, where is delivery number, is instrument abbreviation. Purpose

  20. Unleashing Gen Y: Marketing Mars to Millennials

    NASA Technical Reports Server (NTRS)

    Leahy, Bart D.; Hidalgo, Loretta; Kloberdanz, Cassie

    2007-01-01

    Space advocates need to engage Generation Y (born 1977-1999).This outreach is necessary to recruit the next generation of scientists and engineers to explore Mars. Space advocates in the non-profit, private, and government sectors need to use a combination of technical communication, marketing, and politics, to develop messages that resonate with Gen Y. Until now, space messages have been generated by and for college-educated white males; Gen Y is much more diverse, including as much as one third minorities. Young women, too, need to be reached. My research has shown that messages emphasizing technology, fun, humor, and opportunity are the best means of reaching the Gen Y audience of 60 million (US population is 300 million). The important things space advocates must avoid are talking down to this generation, making false promises, or expecting them to "wait their turn" before they can participate. This is the MTV generation! We need to find ways of engaging Gen Y now to build a future where human beings can live and work on the planet Mars. In addition to the messages themselves, advocates need to keep up with Gen Y' s social networking and use of iPods, cell phones, and the Internet. NASA and space advocacy groups can use these tools for "viral marketing," where young people share targeted space-related information via cell phones or the Internet because they like it. Overall, Gen Y is a socially dynamic and media-savvy group; advocates' space messages need to be sincere, creative, and placed in locations where Gen Y lives. Mars messages must be memorable!

  1. 24/04/2013 Next gen Sequencing technologies

    E-print Network

    Twente, Universiteit

    ;1985 Human genome project proposed Start of the project in 1987 24/04/2013Next gen Sequencing technologies 7 "next gen" patents filed 2003 Human genome project finished 2005 first next gen sequencer available The illumina sequencer family: Genome AnalyzerIIx, HiSeq 2500, HiSeq 2000, HiSeq 1500, HiSeq 1000, Hi

  2. The Integrated Airport: Building a Successful NextGen Testbed

    ScienceCinema

    Christina Frederick-Recascino

    2010-01-08

    This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment.  NextGen refers to the program that will be initiated to modernize the US National Airspace.  As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success.  This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation. 

  3. Quina és la funció del gen clonat?

    Microsoft Academic Search

    Margarita Soriano; Francisca Guerola

    2008-01-01

    Presentem una activitat didàctica complementària per a alumnes de segon de batxillerat. A partir d’una seqüència de nucleòtids del genoma de Paenibacillus barcinonensis determinem la regió codificant d’un gen, la proteïna corresponent i la seva funció. Com a annex s’inclou el guió per a l’alumnat.

  4. An Gen2 Based Security Authentication Protocol for RFID System

    NASA Astrophysics Data System (ADS)

    Yi, Xiaoluo; Wang, Liangmin; Mao, Dongmei; Zhan, Yongzhao

    EPC Class-1 Generation-2 specification(Gen2 in brief) has been accepted as the standard for RFID tags under grant number ISO18000-6C. However, Gen2 does not pay due attention to security. For this reason, a Gen2 based security authentication protocol is developed in this paper. In details, we study the security requirements presented in the current Gen2 based RFID authentication protocols[7-13]. Then we point out the security flaws of Chien's mutual authentication protocol[7], and improve the protocol based on a 11 security requirements. Our improved protocol merely uses CRC and PRNG operations supported by Gen2 and meets the 11 security requirements. In contrast to the similar work [14,15] on Chien's protocol or other Gen2 based schemes, our protocol is more secure and our security analysis is much more comprehensive and qualitative.

  5. ProGen: GPHMM for prokaryotic genomes Sharad Akshar Punuganti

    E-print Network

    Liblit, Ben

    ProGen: GPHMM for prokaryotic genomes Sharad Akshar Punuganti May 10, 2011 Abstract Pro and implemented to train the model and find the genes respectively. ProGen models prokaryotic genome (hence of GPHMMs in the domain of prokaryotic genomes as the genomic structure of prokaryotes is relatively simple

  6. Connector Generator (ConGen) Table of contents

    E-print Network

    Connector Generator (ConGen) Table of contents 1 Overview of Con of ConGen Software connectors are typically used in component-based engineering to model and realize component interconnections. Connectors play an important role both at design time, when they allow

  7. EadGen, un environnement ouvert de production en ligne

    E-print Network

    Paris-Sud XI, Université de

    to the delivering of on-line documents. It automatically transforms learning material into interactive documentsEadGen, un environnement ouvert de production en ligne basé sur XML et XSL-T Marc Nanard, Jocelyne a collaboration between CNAM and CNRS. EadGen offers an open production chain which is fully programmable

  8. TidGen Power System Commercialization Project

    SciTech Connect

    Sauer, Christopher R. [President & CEO] [President & CEO; McEntee, Jarlath [VP Engineering & CTO] [VP Engineering & CTO

    2013-12-30

    ORPC Maine, LLC, a wholly-owned subsidiary of Ocean Renewable Power Company, LLC (collectively ORPC), submits this Final Technical Report for the TidGen® Power System Commercialization Project (Project), partially funded by the U.S. Department of Energy (DE-EE0003647). The Project was built and operated in compliance with the Federal Energy Regulatory Commission (FERC) pilot project license (P-12711) and other permits and approvals needed for the Project. This report documents the methodologies, activities and results of the various phases of the Project, including design, engineering, procurement, assembly, installation, operation, licensing, environmental monitoring, retrieval, maintenance and repair. The Project represents a significant achievement for the renewable energy portfolio of the U.S. in general, and for the U.S. marine hydrokinetic (MHK) industry in particular. The stated Project goal was to advance, demonstrate and accelerate deployment and commercialization of ORPC’s tidal-current based hydrokinetic power generation system, including the energy extraction and conversion technology, associated power electronics, and interconnection equipment capable of reliably delivering electricity to the domestic power grid. ORPC achieved this goal by designing, building and operating the TidGen® Power System in 2012 and becoming the first federally licensed hydrokinetic tidal energy project to deliver electricity to a power grid under a power purchase agreement in North America. Located in Cobscook Bay between Eastport and Lubec, Maine, the TidGen® Power System was connected to the Bangor Hydro Electric utility grid at an on-shore station in North Lubec on September 13, 2012. ORPC obtained a FERC pilot project license for the Project on February 12, 2012 and the first Maine Department of Environmental Protection General Permit issued for a tidal energy project on January 31, 2012. In addition, ORPC entered into a 20-year agreement with Bangor Hydro Electric Company on January 1, 2013 for up to 5 megawatts at a price of $215/MWh, escalating at 2.0% per year.

  9. Gen IV Materials Handbook Functionalities and Operation

    SciTech Connect

    Ren, Weiju [ORNL

    2009-12-01

    This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

  10. Head-Worn Displays for NextGen

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Shelton, Kevin J.; Arthur, J. J.

    2011-01-01

    The operating concepts emerging under the Next Generation air transportation system (NextGen) require new technology and procedures - not only on the ground-side - but also on the flight deck. Flight deck display and decision support technologies are specifically targeted to overcome aircraft safety barriers that might otherwise constrain the full realization of NextGen. One such technology is the very lightweight, unobtrusive head-worn display (HWD). HWDs with an integrated head-tracking system are being researched as they offer significant potential benefit under emerging NextGen operational concepts. Two areas of benefit for NextGen are defined. First, the HWD may be designed to be equivalent to the Head-Up Display (HUD) using Virtual HUD concepts. As such, these operational credits may be provided to significantly more aircraft for which HUD installation is neither practical nor possible. Second, the HWD provides unique display capabilities, such as an unlimited field-of-regard. These capabilities may be integral to emerging NextGen operational concepts, eliminating safety issues which might otherwise constrain the full realization of NextGen. The paper details recent research results, current HWD technology limitations, and future technology development needed to realize HWDs as a enabling technology for NextGen.

  11. Head-worn displays for NextGen

    NASA Astrophysics Data System (ADS)

    Bailey, Randall E.; Shelton, Kevin J.; Arthur, J. J., III

    2011-06-01

    The operating concepts emerging under the Next Generation air transportation system (NextGen) require new technology and procedures - not only on the ground-side - but also on the flight deck. Flight deck display and decision support technologies are specifically targeted to overcome aircraft safety barriers that might otherwise constrain the full realization of NextGen. One such technology is the very lightweight, unobtrusive head-worn display (HWD). HWDs with an integrated head-tracking system are being researched as they offer significant potential benefit under emerging NextGen operational concepts. Two areas of benefit for NextGen are defined. First, the HWD may be designed to be equivalent to the Head-Up Display (HUD) using Virtual HUD concepts. As such, these operational credits may be provided to significantly more aircraft for which HUD installation is neither practical nor possible. Second, the HWD provides unique display capabilities, such as an unlimited field-of-regard. These capabilities may be integral to emerging NextGen operational concepts, eliminating safety issues which might otherwise constrain the full realization of NextGen. The paper details recent research results, current HWD technology limitations, and future technology development needed to realize HWDs as a enabling technology for NextGen.

  12. 1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel Chester French, south side; Maj. Gen. John Reynolds by Charles Grafly, north side. Equestrian Statues: Maj. Gen George B. McClellan by Edward C. Potter, south side; Maj. Gen Winfield S. Hancock by J.Q.A. Ward, north side. The statue at the base of northern inner pedestal is Richard Smith, a type founder and donor of the Memorial. The niches are filled with eight colossal busts including Union generals, admirals, Pennsylvania governor, Memorial's architects (John T. and James H. Windrim), and executor of Smith's will. The frieze is carved with the names of eighty-four prominent Pennsylvania participants in the Civil War. - Smith Memorial Arch, Philadelphia, Philadelphia County, PA

  13. 78 FR 8108 - NextGen Solutions Vendors Guide

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-05

    ...Generation Air Transportation System (NextGen) solutions...of the International Civil Aviation Organization's (ICAO) Aviation System Block Upgrade (ASBU...related to aviation system upgrades) Example: Engineering Services More...

  14. College of Agriculture, Food and Environment GEN General Agriculture

    E-print Network

    MacAdam, Keith

    College of Agriculture, Food and Environment GEN General Agriculture KEY: # = new course * = course IN AGRICULTURE. (3) Anintroductorycourserequiringcriticalanalysisofthemajorsocial. Prereq: Students enrolled in the College of Agriculture; freshmen only in fall semesters and transfers

  15. A Novel Role of Human Holliday Junction Resolvase GEN1 in the Maintenance of Centrosome Integrity

    PubMed Central

    Zhou, Dong-Ping; Xu, Qian; Li, Miao-Miao; Wang, Zhao-Qi; Tong, Wei-Min; Yang, Yun-Gui

    2012-01-01

    The maintenance of genomic stability requires accurate genome replication, repair of DNA damage, and the precise segregation of chromosomes in mitosis. GEN1 possesses Holliday junction resolvase activity in vitro and presumably functions in homology driven repair of DNA double strand breaks. However, little is currently known about the cellular functions of human GEN1. In the present study we demonstrate that GEN1 is a novel centrosome associated protein and we characterize the various phenotypes associated with GEN1 deficiency. We identify an N-terminal centrosome localization signal in GEN1, which is required and sufficient for centrosome localization. We report that GEN1 depletion results in aberrant centrosome numbers associated with the formation of multiple spindle poles in mitosis, an increased number of cells with multi-nuclei, increased apoptosis and an elevated level of spontaneous DNA damage. We find homologous recombination severely impaired in GEN1 deficient cells, suggesting that GEN1 functions as a Holliday junction resolvase in vivo as well as in vitro. Complementation of GEN1 depleted cells with various GEN1 constructs revealed that centrosome association but not catalytic activity of GEN1 is required for preventing centrosome hyper-amplification, formation of multiple mitotic spindles, and multi-nucleation. Our findings provide novel insight into the biological functions of GEN1 by uncovering an important role of GEN1 in the regulation of centrosome integrity. PMID:23166748

  16. Parachloroidium gen. nov. (Trebouxiophyceae, Chlorophyta), a novel genus of coccoid green algae from subaerial corticolous biofilms

    E-print Network

    Parachloroidium gen. nov. (Trebouxiophyceae, Chlorophyta), a novel genus of coccoid green algae. Parachloroidium gen. nov. (Trebouxiophyceae, Chlorophyta), a novel genus of coccoid green algae from subaerial the Parachloroidium strains from other similar green algae. However, ultrastructural characteristics and molecular

  17. Mutation and association analysis of GEN1 in breast cancer susceptibility

    Microsoft Academic Search

    Clare Turnbull; Sarah Hines; Anthony Renwick; Deborah Hughes; David Pernet; Anna Elliott; Sheila Seal; Margaret Warren-Perry; D. Gareth Evans; Diana Eccles; Michael R. Stratton; Nazneen Rahman

    2010-01-01

    GEN1 was recently identified as a key Holliday junction resolvase involved in homologous recombination. Somatic truncating\\u000a GEN1 mutations have been reported in two breast cancers. Together these data led to the proposition that GEN1 is a breast cancer predisposition gene. In this article we have formally investigated this hypothesis. We performed full-gene\\u000a mutational analysis of GEN1 in 176 BRCA1\\/2-negative familial

  18. A Virtual Reality Framework to Optimize Design, Operation and Refueling of GEN-IV Reactors.

    SciTech Connect

    Rizwan-uddin; Nick Karancevic; Stefano Markidis; Joel Dixon; Cheng Luo; Jared Reynolds

    2008-04-23

    many GEN-IV candidate designs are currently under investigation. Technical issues related to material, safety and economics are being addressed at research laboratories, industry and in academia. After safety, economic feasibility is likely to be the most important crterion in the success of GEN-IV design(s). Lessons learned from the designers and operators of GEN-II (and GEN-III) reactors must play a vital role in achieving both safety and economic feasibility goals.

  19. DOE\\/NNSA perspective safeguard by design: GEN III\\/III+ light water reactors and beyond

    Microsoft Academic Search

    Paul Y

    2010-01-01

    An overview of key issues relevant to safeguards by design (SBD) for GEN III\\/IV nuclear reactors is provided. Lessons learned from construction of typical GEN III+ water reactors with respect to SBD are highlighted. Details of SBD for safeguards guidance development for GEN III\\/III+ light water reactors are developed and reported. This paper also identifies technical challenges to extend SBD

  20. GenAnneal: Genetically modified Simulated Annealing

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Lagaris, Isaac E.

    2006-05-01

    A modification of the standard Simulated Annealing (SA) algorithm is presented for finding the global minimum of a continuous multidimensional, multimodal function. We report results of computational experiments with a set of test functions and we compare to methods of similar structure. The accompanying software accepts objective functions coded both in Fortran 77 and C++. Program summaryTitle of program:GenAnneal Catalogue identifier:ADXI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXI_v1_0 Program available from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: The tool is designed to be portable in all systems running the GNU C++ compiler Installation: University of Ioannina, Greece on Linux based machines Programming language used:GNU-C++, GNU-C, GNU Fortran 77 Memory required to execute with typical data: 200 KB No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: No No. of bytes in distributed program, including test data, etc.:84 885 No. of lines in distributed program, including test data, etc.:14 896 Distribution format: tar.gz Nature of physical problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques are frequently trapped in local minima. Global optimization is hence the appropriate tool. For example, solving a non-linear system of equations via optimization, employing a "least squares" type of objective, one may encounter many local minima that do not correspond to solutions (i.e. they are far from zero). Typical running time: Depending on the objective function. Method of solution: We modified the process of step selection that the traditional Simulated Annealing employs and instead we used a global technique based on grammatical evolution.

  1. Competitive Learning for Deep Temporal Networks Robert Gens

    E-print Network

    Anderson, Richard

    Competitive Learning for Deep Temporal Networks Robert Gens Computer Science and Engineering of competitive learning in deep networks for understanding sequential data. Hierarchies of competitive learning algorithms have been found in the brain [1] and their use in deep vision networks has been validated [2

  2. EnGenIUS -- Environmental Genome Informational Utility System.

    PubMed

    Kaplarevic, Mihailo; Murray, Alison E; Cary, Stephen C; Gao, Guang R

    2008-12-01

    Short-insert shotgun sequencing approaches have been applied in recent years to environmental genomic libraries. In the case of complex multispecies microbial communities, there can be many sequence reads that are not incorporated into assemblies, and thus need to be annotated and accessible as single reads. Most existing annotation systems and genome databases accommodate assembled genomes containing contiguous gene-encoding sequences. Thus, a solution is required that can work effectively with environmental genomic annotation information to facilitate data analysis. The Environmental Genome Informational Utility System (EnGenIUS) is a comprehensive environmental genome (metagenome) research toolset that was specifically designed to accommodate the needs of large (> 250 K sequence reads) environmental genome sequencing efforts. The core EnGenIUS modules consist of a set of UNIX scripts and PHP programs used for data preprocessing, an annotation pipeline with accompanying analysis tools, two entity relational databases, and a graphical user interface. The annotation pipeline has a modular structure and can be customized to best fit input data set properties. The integrated entity relational databases store raw data and annotation analysis results. Access to the underlying databases and services is facilitated through a web-based graphical user interface. Users have the ability to browse, upload, download, and analyze preprocessed data, based on diverse search criteria. The EnGenIUS toolset was successfully tested using the Alvinella pompejana epibiont environmental genome data set, which comprises more than 300 K sequence reads. A fully browsable EnGenIUS portal is available at (http://ocean.dbi.udel.edu/) (access code: "guest"). The scope of this paper covers the implementation details and technical aspects of the EnGenIUS toolset. PMID:19090024

  3. AdGVVEGF121.10 (GenVec).

    PubMed

    Basara, N

    2001-06-01

    GenVec, in collaboration with Pfizer (formerly Parke-Davis), is developing AdGVVEGF121.10 (BioBypass), a gene therapy involving the 121-residue isoform of vascular endothelial growth factor (VEGF), licensed from Scios, for the potential treatment of coronary artery disease (CAD) and peripheral vascular disease (PVD) [262000]. By March 2000, phase II trials in CAD had commenced [359531], [359532], [359538]. By August 2000, phase II trials were also underway for PVD [386293]. The initial phase II trial will include approximately 70 patients with severe CAD who are not candidates for bypass surgery and will assess exercise capacity and patient well-being, before and after treatment, as well as safety and drug tolerance [364137]. Scios licensed the gene transfer applications of VEGF121 to GenVec in June 1996 [263381]. In September 1997, GenVec entered into an agreement with Parke-Davis, a subsidiary of Warner-Lambert (now Pfizer), to develop the therapy [262000]. In May 1999, Warner-Lambert signed an agreement with Bioscience for a device for the administration of AdGVVEGF121.10 1325443]. In May 2000, Merrill Lynch predicted a US filing in the first half of 2003 [375962]. In January 2001, AG Edwards predicted the product would generate $70 million in revenues to Pfizer and $12 million in royalties to GenVec in 2005. In February 1999, GenVec was awarded US-05846782, covering vectors for targeting the transfer of therapeutic genes to specific tissues in the human body [316038]. PMID:11572658

  4. GenNet: A Platform for Hybrid Network Experiments

    PubMed Central

    Kispersky, Tilman J.; Economo, Michael N.; Randeria, Pratik; White, John A.

    2011-01-01

    We describe General Network (GenNet), a software plugin for the real time experimental interface (RTXI) dynamic clamp system that allows for straightforward and flexible implementation of hybrid network experiments. This extension to RTXI allows for hybrid networks that contain an arbitrary number of simulated and real neurons, significantly improving upon previous solutions that were limited, particularly by the number of cells supported. The benefits of this system include the ability to rapidly and easily set up and perform scalable experiments with hybrid networks and the ability to scan through ranges of parameters. We present instructions for installing, running and using GenNet for hybrid network experiments and provide several example uses of the system. PMID:21845179

  5. Advanced Vehicle Concepts and Implications for NextGen

    NASA Technical Reports Server (NTRS)

    Blake, Matt; Smith, Jim; Wright, Ken; Mediavilla Ricky; Kirby, Michelle; Pfaender, Holger; Clarke, John-Paul; Volovoi, Vitali; Dorbian, Christopher; Ashok, Akshay; Reynolds, Tom; Waitz, Ian; Hileman, James; Arunachalam, Sarav; Hedrick, Matt; Vempati, Lakshmi; Laroza, Ryan; denBraven, Wim; Henderson, Jeff

    2010-01-01

    This report presents the results of a major NASA study of advanced vehicle concepts and their implications for the Next Generation Air Transportation System (NextGen). Comprising the efforts of dozens of researchers at multiple institutions, the analyses presented here cover a broad range of topics including business-case development, vehicle design, avionics, procedure design, delay, safety, environmental impacts, and metrics. The study focuses on the following five new vehicle types: Cruise-efficient short takeoff and landing (CESTOL) vehicles Large commercial tiltrotor aircraft (LCTRs) Unmanned aircraft systems (UAS) Very light jets (VLJs) Supersonic transports (SST). The timeframe of the study spans the years 2025-2040, although some analyses are also presented for a 3X scenario that has roughly three times the number of flights as today. Full implementation of NextGen is assumed.

  6. J3Gen: A PRNG for Low-Cost Passive RFID

    PubMed Central

    Melià-Seguí, Joan; Garcia-Alfaro, Joaquin; Herrera-Joancomartí, Jordi

    2013-01-01

    Pseudorandom number generation (PRNG) is the main security tool in low-cost passive radio-frequency identification (RFID) technologies, such as EPC Gen2. We present a lightweight PRNG design for low-cost passive RFID tags, named J3Gen. J3Gen is based on a linear feedback shift register (LFSR) configured with multiple feedback polynomials. The polynomials are alternated during the generation of sequences via a physical source of randomness. J3Gen successfully handles the inherent linearity of LFSR based PRNGs and satisfies the statistical requirements imposed by the EPC Gen2 standard. A hardware implementation of J3Gen is presented and evaluated with regard to different design parameters, defining the key-equivalence security and nonlinearity of the design. The results of a SPICE simulation confirm the power-consumption suitability of the proposal. PMID:23519344

  7. GEN IV reactors: Where we are, where we should go

    SciTech Connect

    Locatelli, G. [Univ. of Lincoln, Lincoln School of Engineering, Brayford Pool - Lincoln LN6 7TS (United Kingdom); Mancini, M.; Todeschini, N. [Politecnico di Milano, Dept. of Management, Economics and Industrial Engineering, Via Lambruschini 4/B, Milano (Italy)

    2012-07-01

    GEN IV power plants represent the mid-long term option of the nuclear sector. International literature proposes many papers and reports dealing with these reactors, but there is an evident difference of type and shape of information making impossible each kind of detailed comparison. Moreover, authors are often strongly involved in some particular design; this creates many difficulties in their super-partes position. Therefore it is necessary to put order in the most relevant information to understand strengths and weaknesses of each design and derive an overview useful for technicians and policy makers. This paper presents the state-of the art for GEN IV nuclear reactors providing a comprehensive literature review of the different designs with a relate taxonomy. It presents the more relevant references, data, advantages, disadvantages and barriers to the adoptions. In order to promote an efficient and wide adoption of GEN IV reactors the paper provides the pre-conditions that must be accomplished, enabling factors promoting the implementation and barriers limiting the extent and intensity of its implementation. It concludes outlying the state of the art of the most important R and D areas and the future achievements that must be accomplished for a wide adoption of these technologies. (authors)

  8. Remarks on Peinado et al.'s Analysis of J3Gen.

    PubMed

    Garcia-Alfaro, Joaquin; Herrera-Joancomartí, Jordi; Melià-Seguí, Joan

    2015-01-01

    Peinado et al. analyzed the security of the J3Gen pseudorandom number generator proposed by Melià-Seguí et al., and claimed weaknesses regarding its security properties. They also presented a deterministic attack based on the decimation of the J3Gen output sequences. We show that the assumptions made by Peinado et al. are not correct and that the proposed deterministic attack against J3Gen does not hold in practice. PMID:25781510

  9. Pantanalinema gen. nov. and Alkalinema gen. nov.: novel pseudanabaenacean genera (Cyanobacteria) isolated from saline-alkaline lakes.

    PubMed

    Vieira Vaz, Marcelo Gomes Marçal; Genuário, Diego Bonaldo; Andreote, Ana Paula Dini; Malone, Camila Francieli Silva; Sant'Anna, Célia Leite; Barbiero, Laurent; Fiore, Marli Fátima

    2015-01-01

    The genus Leptolyngbya Anagnostidis & Komárek (1988) was described from a set of strains identified as 'LPP-group B'. The morphology within this group is not particularly informative and underestimates the group's genetic diversity. In the present study, two new pseudanabaenacean genera related to Leptolyngbya morphotypes, Pantanalinema gen. nov. and Alkalinema gen. nov., are described under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants, based on a polyphasic approach. Pantanalinema gen. nov. (type species Pantanalinema rosaneae sp. nov.) has sheaths and trichomes with slight gliding motility, which distinguish this genus from Alkalinema gen. nov. (type species Alkalinema pantanalense sp. nov.), which possesses trichomes arranged in an ornate (interwoven) pattern. 16S rRNA gene sequences of strains of Pantanalinema and Alkalinema exhibited low identity to each other (?91.6?%) and to other sequences from known pseudanabaenacean genera (?94.3 and 93.7?%, respectively). In a phylogenetic reconstruction, six sequences from strains of Pantanalinema and four from strains of Alkalinema formed two separate and robust clades (99?% bootstrap value), with the genera Oculatella and Phormidesmis, respectively, as the closest related groups. 16S-23S rRNA intergenic spacer sequences and secondary structures of strains of Pantanalinema and Alkalinema did not correspond to any previous descriptions. The strains of Pantanalinema and Alkalinema were able to survive and produce biomass at a range of pH (pH 4-11) and were also able to alter the culture medium to pH values ranging from pH 8.4 to 9.9. These data indicate that cyanobacterial communities in underexplored environments, such as the Pantanal wetlands, are promising sources of novel taxa. PMID:25351877

  10. GEN | News Highlights: Scientists Develop High-Capacity Nanoparticles for Targeted Delivery of Drug Cocktails http://www.genengnews.com/gen-news-highlights/scientists-develop-high-capacity-nanoparticles-for-targeted-delivery-of-drug-cocktails/81245016/[4/

    E-print Network

    Brinker, C. Jeffrey

    GEN | News Highlights: Scientists Develop High-Capacity Nanoparticles for Targeted Delivery of Drug Cocktails http://www.genengnews.com/gen-news-highlights/scientists-develop NEWS Blogs Podcasts Webinars Videos New Products Best of the Web Events Jobs Polls App Notes GEN

  11. Specifying and Implementing Visual Process Modeling Languages with DiaGen

    Microsoft Academic Search

    Mark Minas; Berthold Hoffmann

    2001-01-01

    This paper describes how a diagram language can be specified, based on graphs, graph grammars, and transformation rules, and how the diagram editor generator DiaGen generates a diagram editor from such a specification. DiaGen can be ap- plied to practically every visual language, and to visual process modeling languages in particular. This is demonstrated with an editor and animator for

  12. Gen_SuperLU package (version 1.0) by Ahmet Duran and David Saunders

    E-print Network

    Duran, Ahmet

    Gen_SuperLU package (version 1.0) by Ahmet Duran and David Saunders Computer & Information Science from the factorization. Gen_SuperLU was used for the rank computations at "A. Duran, B. D. Saunders Conference on Applied Linear Algebra. July 2003." and "A. Duran, B. D. Saunders and Z. Wan. Rank of Sparse {0

  13. Spatial control of the GEN1 Holliday junction resolvase ensures genome stability

    PubMed Central

    Chan, Ying Wai; West, Stephen C.

    2014-01-01

    Holliday junction (HJ) resolvases are necessary for the processing of persistent recombination intermediates before cell division. Their actions, however, need to be restricted to the late stages of the cell cycle to avoid the inappropriate cleavage of replication intermediates. Control of the yeast HJ resolvase, Yen1, involves phosphorylation changes that modulate its catalytic activity and nuclear import. Here, we show that GEN1, the human ortholog of Yen1, is regulated by a different mechanism that is independent of phosphorylation. GEN1 is controlled exclusively by nuclear exclusion, driven by a nuclear export signal (NES) that restricts GEN1 actions to mitosis when the nuclear membrane breaks down. Construction of a nuclear-localized version of GEN1 revealed that its premature actions partially suppress phenotypes associated with loss of BLM and MUS81, but cause elevated crossover formation. The spatial control of GEN1 therefore contributes to genome stability, by avoiding competition with non-crossover promoting repair pathways. PMID:25209024

  14. Mutation and association analysis of GEN1 in breast cancer susceptibility.

    PubMed

    Turnbull, Clare; Hines, Sarah; Renwick, Anthony; Hughes, Deborah; Pernet, David; Elliott, Anna; Seal, Sheila; Warren-Perry, Margaret; Gareth Evans, D; Eccles, Diana; Stratton, Michael R; Rahman, Nazneen

    2010-11-01

    GEN1 was recently identified as a key Holliday junction resolvase involved in homologous recombination. Somatic truncating GEN1 mutations have been reported in two breast cancers. Together these data led to the proposition that GEN1 is a breast cancer predisposition gene. In this article we have formally investigated this hypothesis. We performed full-gene mutational analysis of GEN1 in 176 BRCA1/2-negative familial breast cancer samples and 159 controls. We genotyped six SNPs tagging the 30 common variants in the transcribed region of GEN1 in 3,750 breast cancer cases and 4,907 controls. Mutation analysis revealed one truncating variant, c.2515_2519delAAGTT, which was present in 4% of cases and 4% of controls. We identified control individuals homozygous for the deletion, demonstrating that the last 69 amino acids of GEN1 are dispensable for its function. We identified 17 other variants, but their frequency did not significantly differ between cases and controls. Analysis of 3,750 breast cancer cases and 4,907 controls demonstrated no evidence of significant association with breast cancer for six SNPs tagging the 30 common GEN1 variants. These data indicate that although it also plays a key role in double-strand DNA break repair, GEN1 does not make an appreciable contribution to breast cancer susceptibility by acting as a high- or intermediate-penetrance breast cancer predisposition gene like BRCA1, BRCA2, CHEK2, ATM, BRIP1 and PALB2 and that common GEN1 variants do not act as low-penetrance susceptibility alleles analogous to SNPs in FGFR2. Furthermore, our analyses demonstrate the importance of undertaking appropriate genetic investigations, typically full gene screening in cases and controls together with large-scale case-control association analyses, to evaluate the contribution of genes to cancer susceptibility. PMID:20512659

  15. Mutation and association analysis of GEN1 in breast cancer susceptibility

    PubMed Central

    Turnbull, Clare; Hines, Sarah; Renwick, Anthony; Hughes, Deborah; Pernet, David; Elliott, Anna; Seal, Sheila; Warren-Perry, Margaret; Evans, D. Gareth; Eccles, Diana; Stratton, Michael R.

    2013-01-01

    GEN1 was recently identified as a key Holliday junction resolvase involved in homologous recombination. Somatic truncating GEN1 mutations have been reported in two breast cancers. Together these data led to the proposition that GEN1 is a breast cancer predisposition gene. In this article we have formally investigated this hypothesis. We performed full-gene mutational analysis of GEN1 in 176 BRCA1/2-negative familial breast cancer samples and 159 controls. We genotyped six SNPs tagging the 30 common variants in the transcribed region of GEN1 in 3,750 breast cancer cases and 4,907 controls. Mutation analysis revealed one truncating variant, c.2515_2519del-AAGTT, which was present in 4% of cases and 4% of controls. We identified control individuals homozygous for the deletion, demonstrating that the last 69 amino acids of GEN1 are dispensable for its function. We identified 17 other variants, but their frequency did not significantly differ between cases and controls. Analysis of 3,750 breast cancer cases and 4,907 controls demonstrated no evidence of significant association with breast cancer for six SNPs tagging the 30 common GEN1 variants. These data indicate that although it also plays a key role in double-strand DNA break repair, GEN1 does not make an appreciable contribution to breast cancer susceptibility by acting as a high- or intermediate-penetrance breast cancer predisposition gene like BRCA1, BRCA2, CHEK2, ATM, BRIP1 and PALB2 and that common GEN1 variants do not act as low-penetrance susceptibility alleles analogous to SNPs in FGFR2. Furthermore, our analyses demonstrate the importance of undertaking appropriate genetic investigations, typically full gene screening in cases and controls together with large-scale case–control association analyses, to evaluate the contribution of genes to cancer susceptibility. PMID:20512659

  16. What Can a Historian Do with AstroGen?

    NASA Astrophysics Data System (ADS)

    Tenn, Joseph S.

    2015-01-01

    "Astrogen", the Astronomy Genealogy Project, is in the development stage. Patterned after the Mathematics Genealogy Project at http://genealogy.math.ndsu.nodak.edu, it will eventually include most of the world's astronomers, past and present, and provide information about their years of life, highest degrees, universities, and thesis titles. There will also be links to online theses, home pages, and obituaries when these are available. Although a few details remain to be worked out before it becomes public, it is possible to make some use of what has already been compiled. I will give an example, comparing graduates of Harvard University, the University of California at Berkeley, and the University of Chicago from different decades, with information about their professional careers and publication records. The author welcomes queries about AstroGen and is seeking more participants.

  17. Reprint of PopGen: A virtual human population generator.

    PubMed

    McNally, Kevin; Cotton, Richard; Hogg, Alex; Loizou, George

    2015-06-01

    The risk assessment of environmental chemicals and drugs is moving towards a paradigm shift in approach which seeks the full replacement animal testing with high throughput, mechanistic, in vitro systems. This new vision will be reliant on the measurement in vitro, of concentration-dependent responses where prolonged excessive perturbations of specific biochemical pathways are likely to lead to adverse health effects in an intact organism. Such an approach requires a framework, into which disparate data generated using in vitro, in silico and in chemico systems, can be integrated and utilised for quantitative in vitro-to-in vivo extrapolation (QIVIVE), ultimately to the human population level. Physiologically based pharmacokinetic (PBPK) models are ideally suited for this and are obligatory in order to translate in vitro concentration-response relationships to an exposure or dose, route and duration regime in people. In this report we describe PopGen a virtual human population generator which is a user friendly, open access web-based application for the prediction of realistic anatomical, physiological and phase 1 metabolic variation in a wide range of healthy human populations. We demonstrate how PopGen can be used for QIVIVE by providing input to a PBPK model, at an appropriate level of detail, to reconstruct exposure from human biomonitoring data. We discuss how the process of exposure reconstruction from blood biomarkers, in general, is analogous to exposure or dose reconstruction from concentration-response measurements made in proposed in vitro cell based systems which are assumed to be surrogates for target organs. PMID:25921244

  18. *Amplexidiscus fenestrafer* n. gen., n. sp. (Coelenterata: Anthozoa), a tropical Indo-Pacific corallimorpharian

    E-print Network

    Fautin, Daphne G.; Hamner, William M.

    1980-06-01

    The sixth genus of corallimorpharian family Actinodiscidae, *Amplexidicus* n.gen., is described. It is distinguished by its numerous short, simple, conical tentacles, and few marginal tentacles. The type species, and currently the only one known...

  19. Cornucoryphe schirmi n. gen. n. sp., an unusual conocoryphid trilobite from the Middle Cambrian of Spain

    Microsoft Academic Search

    K. Sdzuy; E. Liñan

    1996-01-01

    \\u000a Kurzfassung  \\u000a Cornucoryphe n.gen. aus dem Mittel-Kambrium des Kantabrischen Gebirges und Keltiberiens hat zusätzlich zu den Merkmalen vonConocoryphe ein starkes, nach vorn gerichtetes „Horn“ und ausgeprägte Alae.

  20. Hybrid Communication Protocols and Control Algorithms for NextGen Aircraft Arrivals

    E-print Network

    Park, Pangun

    Capacity constraints imposed by current air traffic management technologies and protocols could severely limit the performance of the Next Generation Air Transportation System (NextGen). A fundamental design decision in ...

  1. New records of the Cryphonectriaceae from southern Africa including Latruncellus aurorae gen. sp. nov.

    E-print Network

    New records of the Cryphonectriaceae from southern Africa including Latruncellus aurorae gen. sp in Africa. Surveys in the past 3 y in southern Africa have led to the discovery of cankers with fruiting

  2. Characterizing changes in the immune repertoire of cattle using next-gen sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vertebrate immune systems generate diverse repertoires of antibodies capable of mediating response to a variety of antigens. Next-gen sequencing permits characterization of expressed antibody repertoires at previously unattainable depths of coverage and accuracy. We examined the bovine immunoglobul...

  3. The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research

    Microsoft Academic Search

    MICHAEL J. SANDERSON; Darren Boss; Duhong Chen; KAREN A. CRANSTON; Andre Wehe

    2008-01-01

    As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phy- logenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (http:\\/\\/loco.biosci.arizona.edu\\/pb), which offers a view of GenBank tailored for molecular phylogenetics. The first re- lease of the Browser is computed from 2.6 million sequences representing the taxonomically enriched

  4. GenMapDB: a database of mapped human BAC clones

    Microsoft Academic Search

    Michael Morley; Melissa Arcaro; Joshua Burdick; Raluca Yonescu; Thomas Reid; Ilan R. Kirsch; Vivian G. Cheung

    2001-01-01

    GenMapDB (http:\\/\\/genomics.med.upenn.edu\\/genmapdb) is a repository of human bacterial artificial chromo- some (BAC) clones mapped by our laboratory to sequence-tagged site markers. Currently, GenMapDB contains over 3000 mapped clones that span 19 chromosomes, chromosomes 2, 4, 5, 9-22, X and Y. This database provides positional information about human BAC clones from the RPCI-11 human male BAC library. It also contains restriction

  5. Integrated Design and Production Reference Integration with ArchGenXML V1.00

    SciTech Connect

    Barter, R H

    2004-07-20

    ArchGenXML is a tool that allows easy creation of Zope products through the use of Archetypes. The Integrated Design and Production Reference (IDPR) should be highly configurable in order to meet the needs of a diverse engineering community. Ease of configuration is key to the success of IDPR. The purpose of this paper is to describe a method of using a UML diagram editor to configure IDPR through ArchGenXML and Archetypes.

  6. Mobile payment models and their implications for NextGen MSPs

    Microsoft Academic Search

    Michaël Van Bossuyt; Leo Van Hove

    2007-01-01

    Purpose – This paper aims to provide a first overview of important implications of payment models for next-generation mobile service platforms (NextGen MSPs). Design\\/methodology\\/approach – The starting point of the paper is an existing set of mobile payment models. These models are modified and expanded on in order to be able to highlight implications for NextGen MSPs. Findings – The

  7. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

    Microsoft Academic Search

    Scott W. Doniger; Nathan Salomonis; Kam D Dahlquist; Karen Vranizan; Steven C Lawlor; Bruce R Conklin

    2003-01-01

    MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP http:\\/\\/www.GenMAPP.org. The results are displayed in a searchable browser, allowing the user to rapidly identify GO terms with over-represented numbers of gene-expression changes. Clicking on GO terms generates GenMAPP

  8. NCBI Handout Series | MedGen | Last Update March 9, 2014 Contact: info@ncbi.nlm.nih.gov MedGen: A Medical Genetics Portal

    E-print Network

    Levin, Judith G.

    NCBI Handout Series | MedGen | Last Update March 9, 2014 Contact: info@ncbi.nlm.nih.gov Med from NCBI http://www.ncbi.nlm.nih.gov/medgen National Center for Biotechnology Information · National on the web through its homepage (http://www.ncbi.nlm.nih.gov/medgen) or ac- cessed programmatically via E

  9. Puniceibacterium antarcticum gen. nov., sp. nov., isolated from seawater.

    PubMed

    Liu, Chang; Zhang, Xi-Ying; Su, Hai-Nan; Zhou, Ming-Yang; Chen, Bo; Li, Hai; Chen, Xiu-Lan; Zhao, Dian-Li; Zhou, Bai-Cheng; Shi, Mei; Zhang, Yu-Zhong

    2014-05-01

    A Gram-reaction-negative, aerobic, non-flagellated, rod-shaped bacterium, designated strain SM1211T, was isolated from Antarctic seawater. The isolate grew at 4-35 °C and with 0-10% (w/v) NaCl. It could produce bacteriochlorophyll a, but did not reduce nitrate to nitrite or hydrolyse DNA. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain SM1211T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related to species in the genera Litorimicrobium, Leisingera, Seohaeicola and Phaeobacter with 95.1-96.0% similarities. The predominant cellular fatty acid was C18:1?7c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and two unidentified phospholipids. The genomic DNA G+C content of strain SM1211T was 60.7 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain SM1211T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which the name Puniceibacterium antarcticum gen. nov., sp. nov. is proposed. The type strain of Puniceibacterium antarcticum is SM1211T (=CCTCC AB 2013147T=KACC 16875T). PMID:24478211

  10. GenMAPP 2: new features and resources for pathway analysis

    PubMed Central

    Salomonis, Nathan; Hanspers, Kristina; Zambon, Alexander C; Vranizan, Karen; Lawlor, Steven C; Dahlquist, Kam D; Doniger, Scott W; Stuart, Josh; Conklin, Bruce R; Pico, Alexander R

    2007-01-01

    Background Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displaying these data present a significant challenge. Pathway-based approaches for analyzing microarray data have proven useful for presenting data and for generating testable hypotheses. Results To address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP), a new GenMAPP database schema, and integrated resources for pathway analysis. We have redesigned the GenMAPP database to support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. We have expanded our pathway resources by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. We have implemented a new mode of data visualization to support analysis of complex data, including time-course, single nucleotide polymorphism (SNP), and splicing. GenMAPP version 2 also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages. Conclusion GenMAPP version 2 provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms. PMID:17588266

  11. Initial Investigation of Operational Concept Elements for NASA's NextGen-Airportal Project Research

    NASA Technical Reports Server (NTRS)

    Lohr, Gary; Lee, Jonathan; Poage, James L.; Tobias, Leonard

    2009-01-01

    The NextGen-Airportal Project is organized into three research focus areas: Safe and Efficient Surface Operations, Coordinated Arrival/Departure Operations Management, and Airportal Transition and Integration Management. The content in this document was derived from an examination of constraints and problems at airports for accommodating future increases in air traffic, and from an examination of capabilities envisioned for NextGen. The concepts are organized around categories of constraints and problems and therefore do not precisely match, but generally reflect, the research focus areas. The concepts provide a framework for defining and coordinating research activities that are, and will be, conducted by the NextGen-Airportal Project. The concepts will help the research activities function as an integrated set focused on future needs for airport operations and will aid aligning the research activities with NextGen key capabilities. The concepts are presented as concept elements with more detailed sub-elements under each concept element. For each concept element, the following topics are discussed: constraints and problems being addressed, benefit descriptions, required technology and infrastructure, and an initial list of potential research topics. Concept content will be updated and more detail added as the research progresses. The concepts are focused on enhancing airportal capacity and efficiency in a timeframe 20 to 25 years in the future, which is similar to NextGen's timeframe.

  12. Critical Issues on Materials for Gen-IV Reactors

    SciTech Connect

    Caro, M; Marian, J; Martinez, E; Erhart, P

    2009-02-27

    Within the LDRD on 'Critical Issues on Materials for Gen-IV Reactors' basic thermodynamics of the Fe-Cr alloy and accurate atomistic modeling were used to help develop the capability to predict hardening, swelling and embrittlement using the paradigm of Multiscale Materials Modeling. Approaches at atomistic and mesoscale levels were linked to build-up the first steps in an integrated modeling platform that seeks to relate in a near-term effort dislocation dynamics to polycrystal plasticity. The requirements originated in the reactor systems under consideration today for future sources of nuclear energy. These requirements are beyond the present day performance of nuclear materials and calls for the development of new, high temperature, radiation resistant materials. Fe-Cr alloys with 9-12% Cr content are the base matrix of advanced ferritic/martensitic (FM) steels envisaged as fuel cladding and structural components of Gen-IV reactors. Predictive tools are needed to calculate structural and mechanical properties of these steels. This project represents a contribution in that direction. The synergy between the continuous progress of parallel computing and the spectacular advances in the theoretical framework that describes materials have lead to a significant advance in our comprehension of materials properties and their mechanical behavior. We took this progress to our advantage and within this LDRD were able to provide a detailed physical understanding of iron-chromium alloys microstructural behavior. By combining ab-initio simulations, many-body interatomic potential development, and mesoscale dislocation dynamics we were able to describe their microstructure evolution. For the first time in the case of Fe-Cr alloys, atomistic and mesoscale were merged and the first steps taken towards incorporating ordering and precipitation effects into dislocation dynamics (DD) simulations. Molecular dynamics (MD) studies of the transport of self-interstitial, vacancy and point defect clusters in concentrated Fe-Cr alloys were performed for future diffusion data calculations. A recently developed parallel MC code with displacement allowed us to predict the evolution of the defect microstructures, local chemistry changes, grain boundary segregation and precipitation resulting from radiation enhanced diffusion. We showed that grain boundaries, dislocations and free surfaces are not preferential for alpha-prime precipitation, and explained experimental observations of short-range order (SRO) in Fe-rich FeCr alloys. Our atomistic studies of dislocation hardening allowed us to obtain dislocation mobility functions for BCC pure iron and Fe-Cr and determine for FCC metals the dislocation interaction with precipitates with a description to be used in Dislocation Dynamic (DD) codes. A Synchronous parallel Kinetic Monte Carlo code was developed and tested which promises to expand the range of applicability of kMC simulations. This LDRD furthered the limits of the available science on the thermodynamic and mechanic behavior of metallic alloys and extended the application of physically-based multiscale materials modeling to cases of severe temperature and neutron fluence conditions in advanced future nuclear reactors. The report is organized as follows: after a brief introduction, we present the research activities, and results obtained. We give recommendations on future LLNL activities that may contribute to the progress in this area, together with examples of possible research lines to be supported.

  13. Ctenocheloides attenboroughi n. gen., n. sp. (Crustacea: Decapoda: Axiidea: Ctenochelidae), a new ghost shrimp with pectinate claw fingers from Madagascar

    Microsoft Academic Search

    Arthur Anker

    2010-01-01

    Ctenocheloides, n. gen., is established for a remarkable new species of ctenochelid ghost shrimp, Ctenocheloides attenboroughi, n. gen., n. sp., named after the British naturalist and presenter of numerous BBC nature documentaries, Sir David Attenborough. The holotype, a complete adult female, is presently the only specimen known. It was extracted from a large, mud-cemented piece of rubble collected at a

  14. 78 FR 49507 - OriGen Energy LLC ; Supplemental Notice That Initial Market-Based Rate Filing Includes Request...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-14

    ...DEPARTMENT OF ENERGY Federal Energy Regulatory Commission...ER13-2069-000] OriGen Energy LLC ; Supplemental Notice That Initial Market-Based Rate Filing Includes...proceeding of OriGen Energy LLC's application for market-based rate...

  15. ISSN0249-6399ISRNINRIA/RR--7915--FR+ENG Project-Teams GenScale

    E-print Network

    Boyer, Edmond

    Wohlers , Rumen Andonov , Gunnar W. Klau Project-Teams GenScale Research Report n° 7915 -- version 2ISSN0249-6399ISRNINRIA/RR--7915--FR+ENG RESEARCH REPORT N° 7915 Avril 2012 Project-Teams GenScale Optimal DALI protein structure alignment Inken Wohlers , Rumen Andonov , Gunnar W. Klau hal-00685824

  16. Scopulibacillus darangshiensis gen. nov., sp. nov., isolated from rock.

    PubMed

    Lee, Soon Dong; Lee, Dong Wan

    2009-12-01

    A novel, Gram-positive bacterium, designated DLS-06(T), was isolated from scoria (volcanic ash) under rock on the peak of small mountain (300 m above the sea level; known as Darangshi Oreum) in Jeju, Republic of Korea. The cells of the isolate were aerobic, oxidase-negative, catalase-positive, endospore-forming, non-motile rods. The organism grew at 25 approximately 30 degrees C and initial pH 6.1 approximately 9.1. A neighbour-joining tree based on 16S rRNA gene sequences showed that the organism was related to members of the family "Sporolactobacillaceae" and related taxa. The phylogenetic neighbours were Pullulanibacillus naganoensis (95.2% 16S rRNA gene sequence similarity), Tuberibacillus calidus (95.0%) and Sporolactobacillus (91.8 approximately 94.2%). Levels of 16S rRNA gene sequence similarity of the isolate to representatives of other genera were in the range of 87.2 approximately 93.7%. The organism contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The predominant menaquinone was MK-7. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, an unknown ninhydrin-positive phospholipid, three unknown phospholipids and an unknown lipid. The major fatty acids were anteiso-C(15:0) and anteiso-C(17:0). The G+C content of the DNA was 50.8 mol%. On the basis of the phenotypic and phylogenetic data presented in this study, this organism represents a novel genus and species in the order Bacillales, for which the name Scopulibacillus darangshiensis gen. nov., sp. nov. is proposed. The type strain is DLS-06(T) (=DSM 19377(T) =KCTC 13161(T)). PMID:20127464

  17. Tools for Designing, Evaluating, and Certifying NextGen Technologies and Procedures: Automation Roles and Responsibilities

    NASA Technical Reports Server (NTRS)

    Kanki, Barbara G.

    2011-01-01

    Barbara Kanki from NASA Ames Research Center will discuss research that focuses on the collaborations between pilots, air traffic controllers and dispatchers that will change in NextGen systems as automation increases and roles and responsibilities change. The approach taken by this NASA Ames team is to build a collaborative systems assessment template (CSAT) based on detailed task descriptions within each system to establish a baseline of the current operations. The collaborative content and context are delineated through the review of regulatory and advisory materials, policies, procedures and documented practices as augmented by field observations and interviews. The CSAT is developed to aid the assessment of key human factors and performance tradeoffs that result from considering different collaborative arrangements under NextGen system changes. In theory, the CSAT product may be applied to any NextGen application (such as Trajectory Based Operations) with specified ground and aircraft capabilities.

  18. HIV gp120 vaccine - VaxGen: AIDSVAX, AIDSVAX B/B, AIDSVAX B/E, HIV gp120 vaccine - Genentech, HIV gp120 vaccine AIDSVAX - VaxGen, HIV vaccine AIDSVAX - VaxGen.

    PubMed

    2003-01-01

    VaxGen is developing prophylactic vaccines against HIV-1 consisting of two recombinant gp120 surface proteins from different HIV-1 strains.This profile has been selected from R&D Insight, a pharmaceutical intelligence database produced by Adis International Ltd. The bivalent vaccines [AIDSVAX B/B and AIDSVAX B/E] are being evaluated in two phase III trials. The first multicentre phase III trial of AIDSVAX B/B, was conducted principally in Canada and the US but also at some sites in the Netherlands and Puerto Rico. The trial was completed at the end of 2002. The second phase III trial is being conducted in Thailand with the AIDSVAX B/E vaccine. VaxGen announced in July 2002 that it would be delaying its Biologics License Application (BLA) for AIDSVAX until 2004 to enable the company to fulfil pre-approval manufacturing requirements. AIDSVAX is based on an earlier monovalent gp120 vaccine developed by Genentech that was shown to be safe in humans. VaxGen (formerly Genenvax) was formed as a spin-off company from Genentech with the sole purpose of developing the gp120 vaccine. VaxGen announced in July 2002 that the original License and Supply agreement with Genentech, signed in May 1997, had been amended. Under the revised agreement, Genentech maintains its right to market and sell AIDSVAX in North America, but has relinquished its options to commercialise the vaccine candidate in the rest of the world. Genentech's earlier decision to waive its option to manufacture AIDSVAX has also been formalised in this agreement. Additionally, VaxGen's royalty payments to Genentech for sales to the WHO or UN for underdeveloped nations have also been reduced by up to 50% and Genentech has extended the milestone date associated with VaxGen submitting an NDA. A $US120 million joint venture (Celltrion) has been formed between VaxGen and South Korean investors to manufacture more than 200 million doses of AIDSVAX a year. Celltrion will build and operate two biotechnology manufacturing facilities: a pilot plant in South San Francisco and a larger plant in Incheon, South Korea. VaxGen will retain a 44% interest in the new company, as well as any profit generated by the AIDS vaccine. If AIDSVAX wins regulatory approval, VaxGen is committed to purchasing a minimum of 87 million doses a year. Celltrion announced in July 2002 that it had acquired 24 acres of land in Incheon, South Korea, for the site of its major biologics manufacturing facility. The facility is scheduled to be ready for commercial operation by 2005. The US FDA granted fast-track designations to the two vaccines AIDSVAX B/B and AIDSVAX B/E in December 2002. The study volunteers included 5108 men who have sex with men and 309 at-risk women, all of whom were meant to be HIV negative when they joined the trial. During the 36-month trial, a total of seven injections were administered at months 0, 1, 6, 12, 18, 24 and 30. The ratio of vaccine to placebo recipients was 2:1. On February 24 2003, VaxGen announced that AIDSVAX B/B did not prove effective in the trials conducted in North America and Europe. The study did not show a statistically significant reduction of HIV infection within the study population as a whole, which was the primary endpoint of the trial. However, the study did show a statistically significant reduction of HIV infection in certain vaccinated groups. Trial data indicate that black and Asian volunteers appeared to produce higher levels of antibodies against HIV. White and Hispanic volunteers appeared to develop consistently lower levels of protective antibodies following vaccination. VaxGen intends to conduct additional analyses to confirm if there was a direct correlation between the level of antibodies and the prevention of infection. The company intends to continue development of the vaccine through licensure, including any studies necessary to evaluate the protective riticism in the media about the statistical analysis of the non-Caucasian data, VaxGen issued a statement on 27 February 2003 claiming that the analysis of data from the trial followed a statistica

  19. NextGen Operations in a Simulated NY Area Airspace

    NASA Technical Reports Server (NTRS)

    Smith, Nancy M.; Parke, Bonny; Lee, Paul; Homola, Jeff; Brasil, Connie; Buckley, Nathan; Cabrall, Chris; Chevalley, Eric; Lin, Cindy; Morey, Susan; Omar, Faisal; Rein-Weston, Daphne; Yoo, Hyo-Sang

    2013-01-01

    A human-in-the-loop simulation conducted in the Airspace Operations Laboratory (AOL) at NASA Ames Research Center explored the feasibility of a Next Generation Air Transportation System (NextGen) solution to address airspace and airport capacity limitations in and around the New York metropolitan area. A week-long study explored the feasibility of a new Optimal Profile Descent (OPD) arrival into the airspace as well as a novel application of a Terminal Area Precision Scheduling and Spacing (TAPSS) enhancement to the Traffic Management Advisor (TMA) arrival scheduling tool to coordinate high volume arrival traffic to intersecting runways. In the simulation, four en route sector controllers and four terminal radar approach control (TRACON) controllers managed traffic inbound to Newark International Airport's primary runway, 22L, and its intersecting overflow runway, 11. TAPSS was used to generate independent arrival schedules for each runway and a traffic management coordinator participant adjusted the arrival schedule for each runway 11 aircraft to follow one of the 22L aircraft. TAPSS also provided controller-managed spacing tools (slot markers with speed advisories and timelines) to assist the TRACON controllers in managing the arrivals that were descending on OPDs. Results showed that the tools significantly decreased the occurrence of runway violations (potential go-arounds) when compared with a Baseline condition with no tools. Further, the combined use of the tools with the new OPD produced a peak arrival rate of over 65 aircraft per hour using instrument flight rules (IFR), exceeding the current maximum arrival rate at Newark Liberty International Airport (EWR) of 52 per hour under visual flight rules (VFR). Although the participants rated the workload as relatively low and acceptable both with and without the tools, they rated the tools as reducing their workload further. Safety and coordination were rated by most participants as acceptable in both conditions, although the TRACON Runway Coordinator (TRC) rated neither as acceptable in the Baseline condition. Regarding the role of the TRC, the two TRACON controllers handling the 11 arrivals indicated that the TRC was very much needed in the Baseline condition without tools, but not needed in the condition with tools. This indicates that the tools were providing much of the sequencing and spacing information that the TRC had supplied in the Baseline condition.

  20. Allocatelliglobosispora scoriae gen. nov., sp. nov., isolated from volcanic ash.

    PubMed

    Lee, Dong Wan; Lee, Soon Dong

    2011-02-01

    A novel actinomycete, designated strain Sco-B14(T), was isolated from volcanic ash collected near Darangshi Oreum (a parasitic or satellite volcano) in Jeju, Republic of Korea. The organism formed well-developed, branched substrate mycelium, on which short chains of non-motile spores were arranged singly or in clusters. Aerial mycelium was not produced. Globose bodies were observed. The reverse colour of colonies was light brown to brown. Diffusible pigments were produced on ISP medium 3 and oatmeal-nitrate agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Sco-B14(T) formed a lineage within the family Micromonosporaceae and was distinct from established genera. The 16S rRNA gene sequence similarity of strain Sco-B14(T) to members of related genera of the family was 95.0-95.7?% to type strains of Catellatospora species, 94.7?% to Hamadaea tsunoensis IMSNU 22005(T), 94.7?% to Longispora albida K97-0003(T) and 94.0?% to Catelliglobosispora koreensis LM 042(T). 3-Hydroxydiaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. Whole-cell sugars were glucose, rhamnose, ribose, xylose, arabinose, galactose and mannose. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The menaquinone profile contained MK-10(H(4)) (49?%), MK-9(H(4)) (24?%), MK-10(H(6)) (18?%) and MK-9(H(6)) (9?%). The predominant fatty acids were iso-C(15?:?0) and C(17?:?0). The DNA G+C content was 70.1 mol%. The combination of chemotaxonomic and phylogenetic data clearly separated the isolate from the type strains of all genera in the family Micromonosporaceae. On the basis of the phylogenetic and chemotaxonomic data presented in this paper, strain Sco-B14(T) is considered to represent a novel species of a new genus in the family Micromonosporaceae, for which the name Allocatelliglobosispora scoriae gen. nov., sp. nov. is proposed. The type strain of Allocatelliglobosispora scoriae is Sco-B14(T) (=KCTC 19661(T) =DSM 45362(T)). PMID:20207801

  1. http://www.u-tokyo.ac.jp/fin03/pdf/H21.1.26torihiki.pdf http://www.u-tokyo.ac.jp/gen01/reiki_int/reiki_kaikei/zaimukaikeiininkitei.pdf

    E-print Network

    Miyashita, Yasushi

    .pdf http://www.u-tokyo.ac.jp/gen01/reiki_int/reiki_kaikei/zaimukaikeiininkitei.pdf http://www.u-tokyo.ac.jp/gen01/reiki_int/reiki_kaikei/keiyakujimutoriatukaikite.pdf http://www.u-tokyo.ac.jp/gen01/reiki_int/reiki; 2 3 http://www.u-tokyo.ac.jp/gen01/reiki_int/reiki

  2. Qasimia gen. nov., an early Marattia-like fern from the Permian of Saudi Arabia

    Microsoft Academic Search

    C. R. Hill; R. H. Wagner; A. A. El-Khayal

    1985-01-01

    The marattialean fern Qasimia schyfsmae (Lemoigne) gen. et comb. nov. is described from the Late Permian plant bed at Unayzah in central Saudi Arabia. Although no organic matter is preserved, impregnation of the compressions by iron minerals at an early stage of diagenesis has partly mineralised the synangia and spores. The impressions in a fine-grained shale preserve epidermal cell outlines,

  3. Adm. Greenert and Gen. Amos: A New Naval Era Publication: Proceedings Magazine

    E-print Network

    Adm. Greenert and Gen. Amos: A New Naval Era Publication: Proceedings Magazine Date: June 2013: Proceedings Magazine Date: May 2014 Description: Adm. Greenert and Rear Adm. James M. Foggo III discuss how within the modern age maritime environment. Imminent Domain Publication: Proceedings Magazine Date

  4. Bdellovibrio bacteriovorus gen. et sp. n., a predatory, ectoparasitic, and bacteriolytic microorganism

    Microsoft Academic Search

    H. Stolp; M. P. Starr

    1963-01-01

    Bdellovibrio bacteriovorus, gen. et sp. n., a predatory and ectoparasitic microorganism with lytic activity against susceptible bacteria, is described, as are techniques for isolation and cultivation. These unusual bacteria cause reactions that are similar in their outward manifestations to bacteriophage-induced lysis. Upon plating a mixture of host bacteria and parasites, confluent lysis or single plaque formation occurs, just as in

  5. Two new Stratiomyinae, including Panamamyia gen. nov., from the Neotropical Region (Diptera: Stratiomyidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new species of Hoplitimyia James, H. inbioensis sp. nov., is described from Costa Rica. A new genus, Panamamyia gen. nov., with type species P. silbergliedi sp. nov., is described from Panama. Both taxa are very rare in collections, not having been taken during extensive Malaise trap surveys in ...

  6. ERANOS 2.1 : International Code System for GEN IV Fast Reactor Analysis

    Microsoft Academic Search

    J. M. Ruggieri; J. Tommasi; J. F. Lebrat; C. Suteau; D. Plisson-Rieunier; C. De Saint Jean; G. Rimpault; J. C. Sublet

    2006-01-01

    The aim of the paper is to present the new release of the European Reactor Analysis Optimized code System, ERANOS 2.1. This version has been developed and validated to establish a suitable basis for reliable neutronic calculations of current, as well as advanced fast reactor cores of the GEN IV International Forum. The latest version of the ERANOS code and

  7. InGen of creative production in the health sciences: A workbook companion to innovation generation

    Microsoft Academic Search

    Michael Goodman

    2011-01-01

    InGen of Creative Production in the Health Sciences is a compendium of innovative thinking exercises for individuals and groups, derived from an eclectic array of practical guides for professionals in a variety of fields. Segmented into five subcategories across twenty two chapters, the effort seeks to make techniques for increasing innovative problem solving more accessible to a diverse audience of

  8. Gen X and Y's Attitudes on Using Social Media Platforms for Opinion

    E-print Network

    Jansen, James

    Gen X and Y's Attitudes on Using Social Media Platforms for Opinion Sharing Abstract In this paper, we investigate opinion sharing attitudes and behaviors of 13 ­ 24 year olds on social media platforms. This research utilizes data from 34,514 survey respondents from users of the social media site, my

  9. Concepts et mots lis la famille : , , familia, domus, gens, stirps... 1. La constitution de la famille

    E-print Network

    Gutkin, Boris

    La famille Concepts et mots liés à la famille : , , familia, domus, gens, stirps... 1. La constitution de la famille - Mariage, naissance et mort ; divorce, répudiation ; l'adultère - Parents et enfants ; l'enfant exposé ; le rapt ; l'adoption ; l'inceste - reconnaître et retrouver les siens ; la

  10. USDA Forest Service Gen. Tech. Rep. RMRS-GTR-176. 2006 55 Introduction_______________________

    E-print Network

    Swetnam, Thomas W.

    USDA Forest Service Gen. Tech. Rep. RMRS-GTR-176. 2006 55 Introduction_______________________ Fire.Thevitalrolethatfireplaysincontrollingthe structure of an ecosystem underscores the need for us to increase our knowledge of past and current fire regimes (Morgan and others 1994). Dendrochronological recon- structions of fire histories provide

  11. A Possible Genome To Architecture Project (GenToA) [The Meta-Genome Project?

    E-print Network

    Sloman, Aaron

    concern about the Human Genome project, comparing it with buying a book written in a language nobodyA Possible Genome To Architecture Project (GenToA) [The Meta-Genome Project?] Installed: 2 Aug 2010 can a genome specify an information-processing architecture that grows itself guided by interaction

  12. WWith new research predicting a signifi-cant chance of a massive, tsunami-gen-

    E-print Network

    Tullos, Desiree

    WWith new research predicting a signifi- cant chance of a massive, tsunami-gen- erating earthquake, taking the message of tsunami and earthquake prepared- ness to community meetings and work- shops up of the fault. Given that the last tsunami-generating quake to hit the Oregon coast occurred in 1700, we

  13. Merging and Spacing of Heterogeneous Aircraft in Support of NextGen

    E-print Network

    Egerstedt, Magnus

    Merging and Spacing of Heterogeneous Aircraft in Support of NextGen Rahul Chipalkatty1 , Philip Twu of aircraft. This paper provides a distributed merging and spacing algorithm that maximizes the throughput at the terminal phase of flight, using infor- mation communicated between neighboring aircraft through the ADS

  14. Dematiocladium celtidis gen. sp. nov. (Nectriaceae, Hypocreales), a new genus from Celtis leaf litter in Argentina

    E-print Network

    grown on 2% malt extract agar (MEA; Oxoid), plated onto carnation leaf agar (CLA; Crous, PhillipsDematiocladium celtidis gen. sp. nov. (Nectriaceae, Hypocreales), a new genus from Celtis leaf November 2004; accepted 28 March 2005. A Cylindrocladium-like hyphomycete collected on leaf litter

  15. Febraury 2011 EA Report Brown Bagger 1 When Gen X is in Charge

    E-print Network

    Oliver, Douglas L.

    workers in day-to-day activities. However, more and more Boomers are retiring, leaving the leadership Gen-Xers and younger **Millennial workers, they'll also be leading older workers who are still style for the company's best inter- ests. After all, if these young leaders don't have the right

  16. CottonGen: a genomics, genetics and breeding database for cotton research

    PubMed Central

    Yu, Jing; Jung, Sook; Cheng, Chun-Huai; Ficklin, Stephen P.; Lee, Taein; Zheng, Ping; Jones, Don; Percy, Richard G.; Main, Dorrie

    2014-01-01

    CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST. PMID:24203703

  17. Xylochloris irregularis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga

    E-print Network

    green alga JIR I´ NEUSTUPA 1 *, MAREK ELIA´ S1 , PAVEL SKALOUD 1 , YVONNE NE MCOVA´ 1 AND LENKA irregularis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga. Phycologia 50: 57­66. DOI: 10.2216/08-64.1 The phylogenetic diversity of subaerial coccoid green algae remains

  18. ATLAS vs. NextGen model atmospheres: a combined analysis of synthetic spectral energy distributions

    E-print Network

    E. Bertone; A. Buzzoni; M. Chavez; L. H. Rodriguez-Merino

    2004-06-08

    We carried out a critical appraisal of the two theoretical models, Kurucz' ATLAS9 and PHOENIX/NextGen, for stellar atmosphere synthesis. Our tests relied on the theoretical fit of SEDs for a sample of 334 target stars along the whole spectral-type sequence. The best-fitting physical parameters of stars allowed a calibration of the temperature and bolometric scale. The main conclusions of our analysis are: i) the fitting accuracy of both theoretical libraries drastically degrades at low Teff; ii) comparing with empirical calibrations, both ATLAS and NextGen fits tend to predict slightly warmer Teff, but ATLAS provides in general a sensibly better fit; iii) there is a striking tendency of NextGen to label target stars with an effective temperature and surface gravity in excess with respect to ATLAS. This is a consequence of some ``degeneracy'' in the solution space, partly induced by the different input physics and geometry constraints. A different T(\\tau) vertical structure of stellar atmosphere seems also required for NextGen synthetic SEDs in order to better account for limb-darkening effects in cool stars, as supported by the recent observations of the EROS BLG2000-5 microlensing event.

  19. USDA Forest Service Gen. Tech. Rep. RMRS-GTR-42-vol. 6. 2008 61 Introduction ____________________

    E-print Network

    bioregionwashistoricallyclosed-canopyconiferousand deciduous forest. Coniferous forests are characterized by spruce (Picea spp, P. resinosa, P. rigida, P. banksi- ana)inthenortheasterncoastalandGreatLakesareas. Deciduous forestsUSDA Forest Service Gen. Tech. Rep. RMRS-GTR-42-vol. 6. 2008 61 Introduction

  20. ConceptGen: a gene set enrichment and gene set relation mapping tool

    PubMed Central

    Sartor, Maureen A.; Mahavisno, Vasudeva; Keshamouni, Venkateshwar G.; Cavalcoli, James; Wright, Zachary; Karnovsky, Alla; Kuick, Rork; Jagadish, H.V.; Mirel, Barbara; Weymouth, Terry; Athey, Brian; Omenn, Gilbert S.

    2010-01-01

    Motivation: The elucidation of biological concepts enriched with differentially expressed genes has become an integral part of the analysis and interpretation of genomic data. Of additional importance is the ability to explore networks of relationships among previously defined biological concepts from diverse information sources, and to explore results visually from multiple perspectives. Accomplishing these tasks requires a unified framework for agglomeration of data from various genomic resources, novel visualizations, and user functionality. Results: We have developed ConceptGen, a web-based gene set enrichment and gene set relation mapping tool that is streamlined and simple to use. ConceptGen offers over 20 000 concepts comprising 14 different types of biological knowledge, including data not currently available in any other gene set enrichment or gene set relation mapping tool. We demonstrate the functionalities of ConceptGen using gene expression data modeling TGF-beta-induced epithelial-mesenchymal transition and metabolomics data comparing metastatic versus localized prostate cancers. Availability: ConceptGen is part of the NIH's National Center for Integrative Biomedical Informatics (NCIBI) and is freely available at http://conceptgen.ncibi.org. For terms of use, visit http://portal.ncibi.org/gateway/pdf/Terms%20of%20use-web.pdf Contact: conceptgen@umich.edu; sartorma@umich.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20007254

  1. KORA-gen - Resource for Population Genetics, Controls and a Broad Spectrum of Disease Phenotypes

    Microsoft Academic Search

    H.-E. Wichmann; C. Gieger; T. Illig

    2005-01-01

    KORA-gen is a resource for genetic epidemiological research, based on the KORA platform (Cooperative Health Research in the Region of Augsburg). Biosamples and phenotypic character- istics as well as environmental parameters of 18,000 adults from Augsburg and the surrounding counties are available. The age range of the participants was 25 to 74 years of recruitment and is 30 to 90

  2. \\GenPlan": Combining Genetic Programming and Planning C Henrik Westerberg John Levine

    E-print Network

    Fernandez, Thomas

    of research opening up for planning and promises much excitement and interest. The Genetic Programming\\GenPlan": Combining Genetic Programming and Planning C Henrik Westerberg John Levine 15th solution to planning may lie in applying Genetic Programming to the planning prob- lem. As such a Genetic

  3. J. Phycol. 39, 368378 (2003) LESSARDIA ELONGATA GEN. ET SP. NOV. (DINOFLAGELLATA, PERIDINIALES,

    E-print Network

    Keeling, Patrick

    2003-01-01

    368 J. Phycol. 39, 368­378 (2003) LESSARDIA ELONGATA GEN. ET SP. NOV. (DINOFLAGELLATA, PERIDINIALES, and a new species, Lessardia elongata Saldarriaga et Taylor. Molecular phyloge- netic analyses were performed using the small sub- unit rRNA genes of L. elongata as well as Roscoffia capitata, a member

  4. Distribution, paleoecology, paleoclimatology, and botanical affinity of the Eocene pollen genus Diporoconia n. gen

    Microsoft Academic Search

    N. O. Frederiksen; V. D. Wiggins; I. K. Ferguson; J. Dransfield; C. M. Ager

    1985-01-01

    Diporoconia n. gen. is proposed for diporate subisopolar smooth to perforate pollen grains having annuli or tumescence. Diporoconia iszkaszentgyoergyi (Kedves) n. comb. (the type species), D. nnewiensis (Jan du Chêne et al.) n. comb., and D. spp. 1 and 2 are included in the genus. Distinctive characters of the pollen are the large pores that are at the ends of

  5. Aurapex penicillata gen. sp. nov. from native Miconia theaezans and Tibouchina spp. in Colombia

    E-print Network

    Aurapex penicillata gen. sp. nov. from native Miconia theaezans and Tibouchina spp. in Colombia in Colombia. Fruiting structures of the fungus could be distinguished from those of C. cubensis by their distinctly orange conidiomatal necks. This fungus also was found on several plant species native to Colombia

  6. woMen's AnD genDer stuDies College of Liberal Arts

    E-print Network

    Hartman, Chris

    woMen's AnD genDer stuDies College of Liberal Arts 907-474-6249 www.uaf.edu/women/ Minor only Women's and gender studies offers an interdisciplinary minor focusing on women, girls, and historical to an introductory course and a theory course focusing on women's studies, the minor draws from a variety of other

  7. Elaphrobates euzeti gen. and sp. n. (Digenea: Sanguinicolidae) from Snappers (Lutjanidae) in the Gulf of Mexico

    Microsoft Academic Search

    Stephen A. Bullard; Robin M. Overstreet

    2003-01-01

    Elaphrobates euzeti gen. and sp. n. (Digenea: Sanguinicolidae) infects the heart and branchial vessels of the red snapper (Lutjanus campechanus) and the heart of the gray snapper (Lutjanus griseus) in the Gulf of Mexico. It has ventrolateral tegumental spine rows each consisting of 4-7 spines, an oral sucker with 6-7 concentric spine rows, sinuous posterior ceca extending to the ovary

  8. Algorithmic Traffic Abstraction and its Application to NextGen Generic Airspace

    E-print Network

    of human controller resources. To enable such concepts, traffic characteristics, airspace structuresAlgorithmic Traffic Abstraction and its Application to NextGen Generic Airspace Girishkumar R traffic abstraction algorithms that, given a set of 4D Trajectories (4DTs), extract the traffic structure

  9. GWAS in a box: statistical and visual analytics of structured associations via GenAMap.

    PubMed

    Xing, Eric P; Curtis, Ross E; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

    2014-01-01

    With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap. PMID:24905018

  10. Overview of NASA's Next Generation Air Transportation System (NextGen) Research

    NASA Technical Reports Server (NTRS)

    Swenson, Harry N.

    2009-01-01

    This slide presentation is an overview of the research for the Next Generation Air Transportation System (NextGen). Included is a review of the current air transportation system and the challenges of air transportation research. Also included is a review of the current research highlights and significant accomplishments.

  11. Data Form Number and Name Responsible Office(s) CIHE Data Form Gen

    E-print Network

    Snider, Barry B.

    N E A S C D A T A F O R M S #12;Data Form Number and Name Responsible Office(s) CIHE Data Form Gen: General Information Form President's Office CIHE Data Form 1: Statement of Financial Position Executive Vice President CIHE Data Form 2-1: Statement of Unrestricted Revenues and Expenses Executive Vice

  12. Heterorhabditidoides chongmingensis gen. nov., sp. nov. (Rhabditida: Rhabditidae), a novel member of the entomopathogenic nematodes

    Microsoft Academic Search

    Chongxing Zhang; Jingrui Liu; Mingxu Xu; Jie Sun; Shouyun Yang; Xianhui An; Guofu Gao; Maosong Lin; Ren Lai; Ziyi He; Yidong Wu; Keyun Zhang

    2008-01-01

    During a recent soil sample survey in Eastern China, a new entomopathogenic nematode species, collected from the Chongming Islands in the southern–eastern area of Shanghai, was discovered. Morphological characteristics of different developmental stages of the nematode combined with molecular data showed that this nematode is a new genus of Rhabditidae, and described as Heterorhabditidoides chongmingensis gen. nov., sp. nov., for

  13. The security of EPC Gen2 compliant RFID Mike Burmester1

    E-print Network

    Burmester, Mike

    The security of EPC Gen2 compliant RFID protocols Mike Burmester1 and Breno de Medeiros2 1-Random Number Generator and a 16-bit Cyclic Redundancy Code. Recently two EPCGen2 compliant protocols that ad issue of supporting security in EPCGen2 compliant proto- cols and propose two RFID protocols

  14. USDA Forest Service Gen. Tech. Rep. PSW-110. 1989. 305 SESSION G: WILDLIFE II: MANAGING WILDLIFE

    E-print Network

    Standiford, Richard B.

    USDA Forest Service Gen. Tech. Rep. PSW-110. 1989. 305 SESSION G: WILDLIFE II: MANAGING WILDLIFE as having the greatest biological diversity and the highest productivity among wildlife habitats. Riparian invertebrate, fish, amphibian, reptile, bird, and mammal species. A significant number of wildlife species

  15. Environmental Information for the U.S. Next Generation Air Transportation System (NextGen)

    NASA Astrophysics Data System (ADS)

    Murray, J.; Miner, C.; Pace, D.; Minnis, P.; Mecikalski, J.; Feltz, W.; Johnson, D.; Iskendarian, H.; Haynes, J.

    2009-09-01

    It is estimated that weather is responsible for approximately 70% of all air traffic delays and cancellations in the United States. Annually, this produces an overall economic loss of nearly 40B. The FAA and NASA have determined that weather impacts and other environmental constraints on the U.S. National Airspace System (NAS) will increase to the point of system unsustainability unless the NAS is radically transformed. A Next Generation Air Transportation System (NextGen) is planned to accommodate the anticipated demand for increased system capacity and the super-density operations that this transformation will entail. The heart of the environmental information component that is being developed for NextGen will be a 4-dimensional data cube which will include a single authoritative source comprising probabilistic weather information for NextGen Air Traffic Management (ATM) systems. Aviation weather constraints and safety hazards typically comprise meso-scale, storm-scale and microscale observables that can significantly impact both terminal and enroute aviation operations. With these operational impacts in mind, functional and performance requirements for the NextGen weather system were established which require significant improvements in observation and forecasting capabilities. This will include satellite observations from geostationary and/or polar-orbiting hyperspectral sounders, multi-spectral imagers, lightning mappers, space weather monitors and other environmental observing systems. It will also require improved in situ and remotely sensed observations from ground-based and airborne systems. These observations will be used to better understand and to develop forecasting applications for convective weather, in-flight icing, turbulence, ceilings and visibility, volcanic ash, space weather and the environmental impacts of aviation. Cutting-edge collaborative research efforts and results from NASA, NOAA and the FAA which address these phenomena are summarized. In 2003, a Joint Planning and Development Office (JPDO) was established by public law to meet the significant challenges that NextGen presents. JPDO partners were chartered which include, but are not limited to, the Federal Aviation Administration (FAA), the National Oceanic and Atmospheric Administration (NOAA), the National Aeronautics and Space Administration (NASA), the Department of Defense (DOD) and broad elements of academia and the aviation industry. This paper provides the aviation meteorology community with useful insight on salient NextGen environmental information requirements that have been developed by the JPDO Weather Working Group's Environmental Information Team. These efforts will help to define observation and forecast systems needed to support NextGen and to develop the operational applications for NextGen aviation weather information. Another major goal of this paper is to inform the international weather community of our research progress and plans for NextGen, to foster research collaboration with our colleagues, and to exchange information to maximize success of NextGen, SESAR and related initiatives world-wide.

  16. Transduction of Photoreceptors With Equine Infectious Anemia Virus Lentiviral Vectors: Safety and Biodistribution of StarGen for Stargardt Disease

    PubMed Central

    Binley, Katie; Widdowson, Peter; Loader, Julie; Kelleher, Michelle; Iqball, Sharifah; Ferrige, Georgina; de Belin, Jackie; Carlucci, Marie; Angell-Manning, Diana; Hurst, Felicity; Ellis, Scott; Miskin, James; Fernandes, Alcides; Wong, Paul; Allikmets, Rando; Bergstrom, Christopher; Aaberg, Thomas; Yan, Jiong; Kong, Jian; Gouras, Peter; Prefontaine, Annick; Vezina, Mark; Bussieres, Martin; Naylor, Stuart; Mitrophanous, Kyriacos A.

    2013-01-01

    Purpose. StarGen is an equine infectious anemia virus (EIAV)-based lentiviral vector that expresses the photoreceptor-specific adenosine triphosphate (ATP)-binding cassette transporter (ABCA4) protein that is mutated in Stargardt disease (STGD1), a juvenile macular dystrophy. EIAV vectors are able to efficiently transduce rod and cone photoreceptors in addition to retinal pigment epithelium in the adult macaque and rabbit retina following subretinal delivery. The safety and biodistribution of StarGen following subretinal delivery in macaques and rabbits was assessed. Methods. Regular ophthalmic examinations, IOP measurements, ERG responses, and histopathology were carried out in both species to compare control and vector-treated eyes. Tissue and fluid samples were obtained to evaluate the persistence, biodistribution, and shedding of the vector following subretinal delivery. Results. Ophthalmic examinations revealed a slightly higher level of inflammation in StarGen compared with control treated eyes in both species. However, inflammation was transient and no overt toxicity was observed in StarGen treated eyes and there were no abnormal clinical findings. There was no StarGen-associated rise in IOP or abnormal ERG response in either rabbits or macaques. Histopathologic examination of the eyes did not reveal any detrimental changes resulting from subretinal administration of StarGen. Although antibodies to StarGen vector components were detected in rabbit but not macaque serum, this immunologic response did not result in any long-term toxicity. Biodistribution analysis demonstrated that the StarGen vector was restricted to the ocular compartment. Conclusions. In summary, these studies demonstrate StarGen to be well tolerated and localized following subretinal administration. PMID:23620430

  17. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework.

    PubMed

    Parks, Donovan H; Mankowski, Timothy; Zangooei, Somayyeh; Porter, Michael S; Armanini, David G; Baird, Donald J; Langille, Morgan G I; Beiko, Robert G

    2013-01-01

    GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis. PMID:23922841

  18. 75 FR 5780 - Green Borders Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-04

    ...Regulatory Commission [Docket No. EL10-36-000] Green Borders Geothermal, LLC, Complainant, v. Terra-Gen...2010. Take notice that on January 25, 2010, Green Borders Geothermal, LLC (Green Borders) filed a formal complaint against...

  19. Squamasnema amazonica n. gen. n. sp. (Heligmonellinae): A new parasite of Proechimys roberti (Rodentia: Echimyidae) in the Brazilian Amazon.

    PubMed

    Cordeiro, Helrik da Costa; Melo, Francisco Tiago de Vasconcelos; Furtado, Adriano Penha; Giese, Elane Guerreiro; Maldonado, Arnaldo; Santos, Jeannie Nascimento Dos

    2015-08-01

    A new species of nematode, Squamasnema amazonica n. gen. n. sp., is described based on specimens found parasitizing the small intestine of Proechimys roberti (Rodentia: Echimyidae) collected during a survey of the fauna of Tapirapé-Aquirí National Forest (Brazil, Eastern Brazilian Amazon). The nematodes were fixed and processed for light microscopy and scanning electron microscopy (SEM). These nematodes were classified under the family Heligmonellidae and the subfamily Heligmonellinae. Although several species in the family Heligmonellidae exhibit discontinuous ridges, Squamasnema n. gen. and Trichotravassosia are the only genera with columns of scales along their entire body, as an apomorphy of the synlophe. Squamasnema n. gen. has columns of cuticular cells along its body, except for on the left flank, and exhibits a synlophe with no size gradient or inclination and does not present chitinized structures supporting the synlophe. Therefore, due to these morphological differences of Squamasnema n. gen., the creation of a new genus was necessary. PMID:25910627

  20. Pharmacogenetic approaches to hypertension therapy: design and rationale for the Genetics of Hypertension Associated Treatment (GenHAT) study

    Microsoft Academic Search

    DK Arnett; E Boerwinkle; BR Davis; J Eckfeldt; CE Ford; H Black

    2002-01-01

    The Genetics of Hypertension Associated Treatment (GenHAT) study will determine whether variants in hypertension susceptibility genes interact with antihypertensive medication to modify coronary heart disease (CHD) risk in hypertensives. GenHAT is an ancillary study of the Antihypertensive and Lipid Lowering Treatment to Prevent Heart Attack Trial, ALLHAT, a double-blind, randomized trial of 42 418 hypertensives, 55 years of age or

  1. Revision of J3Gen and Validity of the Attacks by Peinado et al.

    PubMed

    Peinado, Alberto; Munilla, Jorge; Fúster-Sabater, Amparo

    2015-01-01

    This letter is the reply to: Remarks on Peinado et al.'s Analysis of J3Gen by J. Garcia-Alfaro, J. Herrera-Joancomartí and J. Melià-Seguí published in Sensors 2015, 15, 6217-6220. Peinado et al. cryptanalyzed the pseudorandom number generator proposed by Melià-Seguí et al., describing two possible attacks. Later, Garcia-Alfaro claimed that one of this attack did not hold in practice because the assumptions made by Peinado et al. were not correct. This letter reviews those remarks, showing that J3Gen is anyway flawed and that, without further information, the interpretation made by Peinado et al. seems to be correct. PMID:26007740

  2. Towards Structuring Unstructured GenBank Metadata for Enhancing Comparative Biological Studies

    PubMed Central

    Chen, Elizabeth S.; Sarkar, Indra Neil

    2011-01-01

    Within large sequence repositories such as GenBank there is a wealth of metadata providing contextual information that may enhance search and retrieval of relevant sequences for a range of subsequent analyses. One challenge is the use of free-text in these metadata fields where approaches are needed to extract, structure, and encode essential information. The goal of the present study was to explore the feasibility of using a combination of existing resources for annotating unstructured GenBank metadata, initially focusing on the “host” and “isolation_source” fields. This paper summarizes early results for 10 host organisms that include a characterization of associated isolation sources with respect to biomedical ontologies and semantic types. The findings from this preliminary study provide insights to the rich amount of information captured within these unstructured metadata, guidance for addressing the challenges and issues encountered, and highlight the potential value for enriching comparative biological studies towards improving human health. PMID:22211174

  3. jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors.

    PubMed

    Liu, Xiaoming

    2012-08-01

    1. Next-generation sequencing (NGS) is being increasingly used in ecological and evolutionary studies. Though promising, NGS is known to be error-prone. Sequencing error can cause significant bias for population genetic analysis of a sequence sample.2. We present jPopGen Suite, an integrated tool for population genetic analysis of DNA polymorphisms from nucleotide sequences. It is specially designed for data with a non-negligible error rate, although it serves well for "error-free" data. It implements several methods for estimating the population mutation rate, population growth rate, and conducting neutrality tests.3. jPopGen Suite facilitates the population genetic analysis of NGS data in various applications, and is freely available for non-commercial users at http://sites.google.com/site/jpopgen/. PMID:22905315

  4. Revision of J3Gen Validity of the Attacks by Peinado et al.

    PubMed Central

    Peinado, Alberto; Munilla, Jorge; Fúster-Sabater, Amparo

    2015-01-01

    This letter is the reply to: Remarks on Peinado et al.’s Analysis of J3Gen by J. Garcia-Alfaro, J. Herrera-Joancomartí and J. Melià-Seguí published in Sensors 2015, 15, 6217–6220. Peinado et al. cryptanalyzed the pseudorandom number generator proposed by Melià-Seguí et al., describing two possible attacks. Later, Garcia-Alfaro claimed that one of this attack did not hold in practice because the assumptions made by Peinado et al. were not correct. This letter reviews those remarks, showing that J3Gen is anyway flawed and that, without further information, the interpretation made by Peinado et al. seems to be correct. PMID:26007740

  5. Dual-track CCS stakeholder engagement: Lessons learned from FutureGen in Illinois

    Microsoft Academic Search

    Gretchen Hund; Sallie E. Greenberg

    2011-01-01

    FutureGen, as originally planned, was to be the world’s first coal-fueled, near-zero emissions power plant with fully integrated, 90% carbon capture and storage (CCS). From conception through siting and design, it enjoyed strong support from multiple stakeholder groups, which benefited the overall project. Understanding the stakeholder engagement process for this project provides valuable insights into the design of stakeholder programs

  6. Genetical Genomic Analysis of Complex Phenotypes Using the PhenoGen Website

    Microsoft Academic Search

    Beth BennettLaura; Laura M. Saba; Cheryl K. Hornbaker; Katerina J. Kechris; Paula Hoffman; Boris Tabakoff

    2011-01-01

    Our laboratory has developed an online interactive resource called PhenoGen (http:\\/\\/phenogen.ucdenver.edu) which provides an archive of brain and other organ gene expression data from a panel of 20 common inbred mouse strains,\\u000a and three recombinant inbred (RI) panels (two mouse and one rat). DNA microarray data can also be uploaded to the site where\\u000a numerous analytical tools can be implemented.

  7. GrGen: A Fast SPO-Based Graph Rewriting Tool

    Microsoft Academic Search

    Rubino Geiß; Gernot Veit Batz; Daniel Grund; Sebastian Hack; Adam Szalkowski

    2006-01-01

    WWW home page: http:\\/\\/www.info.uni-karlsruhe.de\\/~rubino Abstract. Graph rewriting is a powerful technique that requires graph pattern matching, which is an NP-complete problem. We present Gr- Gen, a generative programming system for graph rewriting, which ap- plies heuristic optimizations. According to Varro's benchmark it is at least one order of magnitude faster than any other tool known to us. Our graph rewriting

  8. ShieldGen: Automatic Data Patch Generation for Unknown Vulnerabilities with Informed Probing

    Microsoft Academic Search

    Weidong Cui; Marcus Peinado; Helen J. Wang; Michael E. Locasto

    2007-01-01

    In this paper, we present ShieldGen, a system for au- tomatically generating a data patch or a vulnerability signature for an unknown vulnerability, given a zero-day attack instance. The key novelty in our work is that we leverage knowledge of the data format to generate new potential attack instances, which we call probes, and use a zero-day detector as an

  9. Generalized background error covariance matrix model (GEN_BE v2.0)

    NASA Astrophysics Data System (ADS)

    Descombes, G.; Auligné, T.; Vandenberghe, F.; Barker, D. M.; Barré, J.

    2015-03-01

    The specification of state background error statistics is a key component of data assimilation since it affects the impact observations will have on the analysis. In the variational data assimilation approach, applied in geophysical sciences, the dimensions of the background error covariance matrix (B) are usually too large to be explicitly determined and B needs to be modeled. Recent efforts to include new variables in the analysis such as cloud parameters and chemical species have required the development of the code to GENerate the Background Errors (GEN_BE) version 2.0 for the Weather Research and Forecasting (WRF) community model. GEN_BE allows for a simpler, flexible, robust, and community-oriented framework that gathers methods used by some meteorological operational centers and researchers. We present the advantages of this new design for the data assimilation community by performing benchmarks of different modeling of B and showing some of the new features in data assimilation test cases. As data assimilation for clouds remains a challenge, we present a multivariate approach that includes hydrometeors in the control variables and new correlated errors. In addition, the GEN_BE v2.0 code is employed to diagnose error parameter statistics for chemical species, which shows that it is a tool flexible enough to implement new control variables. While the generation of the background errors statistics code was first developed for atmospheric research, the new version (GEN_BE v2.0) can be easily applied to other domains of science and chosen to diagnose and model B. Initially developed for variational data assimilation, the model of the B matrix may be useful for variational ensemble hybrid methods as well.

  10. Acidiphilium cryptum gen. nov., nov., Heterotrophic Bacterium From Acidic Mineral Environments

    Microsoft Academic Search

    ARTHUR P. HARRISON

    Acidiphilium gen. nov. is comprised of gram-negative, aerobic, mesophilic, rod- shaped bacteria that grow in lean organic media between pH 1.9 and 5.9 but not at pH 6.1, Small amounts of organic substrates are required for growth, but high concentrations inhibit growth, especially the organic digests used in conventional bacteriological media. Sodium acetate is strongly inhibitory at a concentration of

  11. Description of Caldicellulosiruptor saccharolyticus gen. nov., sp. nov: an obligately anaerobic, extremely thermophilic, cellulolytic bacterium.

    PubMed

    Rainey, F A; Donnison, A M; Janssen, P H; Saul, D; Rodrigo, A; Bergquist, P L; Daniel, R M; Stackebrandt, E; Morgan, H W

    1994-07-15

    A new obligately anaerobic, extremely thermophilic, cellulolytic bacterium is described. The strain designated Tp8T 6331 is differentiated from thermophilic cellulolytic clostridia on the basis of physiological characteristics and phylogenetic position within the Bacillus/Clostridium subphylum of the Gram-positive bacteria. Strain Tp8T 6331 is assigned to a new genus Caldicellulosiruptor, as Caldicellulosiruptor saccharolyticus gen., nov., sp. nov. PMID:8076802

  12. Complexity analysis of the Next Gen Air Traffic Management System: trajectory based operations.

    PubMed

    Lyons, Rhonda

    2012-01-01

    According to Federal Aviation Administration traffic predictions currently our Air Traffic Management (ATM) system is operating at 150 percent capacity; forecasting that within the next two decades, the traffic with increase to a staggering 250 percent [17]. This will require a major redesign of our system. Today's ATM system is complex. It is designed to safely, economically, and efficiently provide air traffic services through the cost-effective provision of facilities and seamless services in collaboration with multiple agents however, contrary the vision, the system is loosely integrated and is suffering tremendously from antiquated equipment and saturated airways. The new Next Generation (Next Gen) ATM system is designed to transform the current system into an agile, robust and responsive set of operations that are designed to safely manage the growing needs of the projected increasingly complex, diverse set of air transportation system users and massive projected worldwide traffic rates. This new revolutionary technology-centric system is dynamically complex and is much more sophisticated than it's soon to be predecessor. ATM system failures could yield large scale catastrophic consequences as it is a safety critical system. This work will attempt to describe complexity and the complex nature of the NextGen ATM system and Trajectory Based Operational. Complex human factors interactions within Next Gen will be analyzed using a proposed dual experimental approach designed to identify hazards, gaps and elicit emergent hazards that would not be visible if conducted in isolation. Suggestions will be made along with a proposal for future human factors research in the TBO safety critical Next Gen environment. PMID:22317416

  13. Dual-track CCS stakeholder engagement: Lessons learned from FutureGen in Illinois

    USGS Publications Warehouse

    Hund, G.; Greenberg, S.E.

    2011-01-01

    FutureGen, as originally planned, was to be the world's first coal-fueled, near-zero emissions power plant with fully integrated, 90% carbon capture and storage (CCS). From conception through siting and design, it enjoyed strong support from multiple stakeholder groups, which benefited the overall project. Understanding the stakeholder engagement process for this project provides valuable insights into the design of stakeholder programs for future CCS projects. FutureGen is one of few projects worldwide that used open competition for siting both the power plant and storage reservoir. Most site proposals were coordinated by State governments. It was unique in this and other respects relative to the site selection method used on other DOE-supported projects. At the time of site selection, FutureGen was the largest proposed facility designed to combine an integrated gasification combined cycle (IGCC) coal-fueled power plant with a CCS system. Stakeholder engagement by states and the industry consortium responsible for siting, designing, building, and operating the facility took place simultaneously and on parallel tracks. On one track were states spearheading state-wide site assessments to identify candidate sites that they wanted to propose for consideration. On the other track was a public-private partnership between an industry consortium of thirteen coal companies and electric utilities that comprised the FutureGen Alliance (Alliance) and the U.S. Department of Energy (DOE). The partnership was based on a cooperative agreement signed by both parties, which assigned the lead for siting to the Alliance. This paper describes the stakeholder engagement strategies used on both of these tracks and provides examples from the engagement process using the Illinois semi-finalist sites. ?? 2011 Published by Elsevier Ltd.

  14. A Thiococcus sp. nov. gen., its pigments and internal membrane system

    Microsoft Academic Search

    K. E. EIIVII-IJELLEiV; Heidi Steensland; J. Traetteberg

    1967-01-01

    A Thiococcus sp. nov. gen., the first Thiorhodaceae known to contain bacteriochlorophyll b, was isolated from river mud using filtered light above 900 mµ as the selecting agent in enrichments. The orange-brown colour of the immotile, Gram-negative, photolithotrophic cocci is due to two new carotenoids, 3,4,3',4'-tetrahydrospirilloxanthin and 3,4,3',4'-tetrahydrospirilloxanthinal. The photosynthetic pigments appear to be associated with a unique internal membrane

  15. Yamaguchia toyensis n. sp., n. gen. (Annelida, Clitellata, Lumbriculidae) from profundal lake habitat in Japan

    USGS Publications Warehouse

    Fend, S.V.; Ohtaka, A.

    2004-01-01

    Yamaguchia toyensis n. sp., n. gen. is described from an oligotrophic caldera lake, Lake Toya, Hokkaido, Japan. Although the taxonomic affinities are unknown, the genus differs from all other Lumbriculidae in having the combination of testes and atria in X, a single, prosoporous male funnel per atrium, and spermathecae in XI. Unlike other Japanese lakes that have thus far been surveyed, Lake Toya supports abundant populations of lumbriculids in the profundal benthos.

  16. Enhanced and Synthetic Vision for Terminal Maneuvering Area NextGen Operations

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Norman, R. Michael; Williams, Steven P.; Arthur, Jarvis J., III; Shelton, Kevin J.; Prinzel, Lawrence J., III

    2011-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility ground (taxi) operations and approach/landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O Hare environment. Various scenarios tested the potential for EFVS for operations in visibility as low as 1000 ft runway visibility range (RVR) and SVS to enable lower decision heights (DH) than can currently be flown today. Expanding the EFVS visual segment from DH to the runway in visibilities as low as 1000 RVR appears to be viable as touchdown performance was excellent without any workload penalties noted for the EFVS concept tested. A lower DH to 150 ft and/or possibly reduced visibility minima by virtue of SVS equipage appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  17. Structures and stability of metal-doped GenM (n = 9, 10) clusters

    NASA Astrophysics Data System (ADS)

    Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; Zhao, Li-Zhen; Zang, Qing-Jun; Wang, C. Z.; Ho, K. M.

    2015-06-01

    The lowest-energy structures of neutral and cationic GenM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge9 and Ge10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Gen clusters. However, the neutral and cationic FeGe9,10,MnGe9,10 and Ge10Al are cage-like with the metal atom encapsulated inside. Such cage-like transition metal doped Gen clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge9,10Fe and Ge9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.

  18. Leptojacobus dorci n. gen., n. sp. (Nematoda: Diplogastridae), an Associate of Dorcus Stag Beetles (Coleoptera: Lucanidae).

    PubMed

    Kanzaki, Natsumi; Ragsdale, Erik J; Susoy, Vladislav; Sommer, Ralf J

    2014-03-01

    A new species of diplogastrid nematode, Leptojacobus dorci n. gen., n. sp., was isolated from adults of the stag beetle Dorcus ritsemae (Coleoptera: Lucanidae) that were purchased from a pet shop in Japan. Leptojacobus n. gen. is circumscribed by a very thin, delicate body and by a small stoma with minute armature. A combination of other stomatal characters, namely the division of the cheilostom into adradial plates, the symmetry of the subventral stegostomatal sectors, and the presence of a thin, conical dorsal tooth, further distinguishes Leptojacobus n. gen. from other genera of Diplogastridae. Phylogenetic analysis of nearly full-length SSU rRNA sequences support the new species, together with an isolate identified previously as Koerneria luziae, to be excluded from a clade including all other molecularly characterized diplogastrids with teeth and stomatal dimorphism. Therefore, the new species will be of importance for reconstruction of ancestral character histories in Diplogastridae, a family circumscribed by a suite of feeding-related novelties. PMID:24644371

  19. The PhenoGen Informatics website: tools for analyses of complex traits

    PubMed Central

    Bhave, Sanjiv V; Hornbaker, Cheryl; Phang, Tzu L; Saba, Laura; Lapadat, Razvan; Kechris, Katherina; Gaydos, Jeanette; McGoldrick, Daniel; Dolbey, Andrew; Leach, Sonia; Soriano, Brian; Ellington, Allison; Ellington, Eric; Jones, Kendra; Mangion, Jonathan; Belknap, John K; Williams, Robert W; Hunter, Lawrence E; Hoffman, Paula L; Tabakoff, Boris

    2007-01-01

    Background With the advent of "omics" (e.g. genomics, transcriptomics, proteomics and phenomics), studies can produce enormous amounts of data. Managing this diverse data and integrating with other biological data are major challenges for the bioinformatics community. Comprehensive new tools are needed to store, integrate and analyze the data efficiently. Description The PhenoGen Informatics website is a comprehensive toolbox for storing, analyzing and integrating microarray data and related genotype and phenotype data. The site is particularly suited for combining QTL and microarray data to search for "candidate" genes contributing to complex traits. In addition, the site allows, if desired by the investigators, sharing of the data. Investigators can conduct "in-silico" microarray experiments using their own and/or "shared" data. Conclusion The PhenoGen website provides access to tools that can be used for high-throughput data storage, analyses and interpretation of the results. Some of the advantages of the architecture of the website are that, in the future, the present set of tools can be adapted for the analyses of any type of high-throughput "omics" data, and that access to new tools, available in the public domain or developed at PhenoGen, can be easily provided. PMID:17760997

  20. GenColors-based comparative genome databases for small eukaryotic genomes

    PubMed Central

    Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

    2013-01-01

    Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources. PMID:23193285

  1. Swedish Plectida (Nematoda). Part 6. Neocamacolaimus parasiticus gen. n., sp. n.

    PubMed

    Holovachov, Oleksandr; Boström, Sven

    2014-01-01

    A new genus Neocamacolaimus gen. n., with one new species N. parasiticus gen. n., sp. n. is described from the benthic polychaete Sphaerosyllis cf. hystrix collected in the Skagerrak off the west coast of Sweden. Neocamacolaimus gen. n. is placed in the family Camacolaimidae and is particularly characterised by having annulated cuticle with lateral alae; setiform cephalic sensilla located at level with amphids; amphidial fovea ventrally spiral; buccal cavity without armament; pharynx muscular; nerve ring located at base of pharynx; male reproductive system diorchic with outstretched testes; spicules weakly arcuate with straight manubrium; gubernaculum absent; alveolar supplements located in the pharyngeal region; tubular supplements absent; tail conoid; caudal glands and spinneret present. Juveniles of this genus are particularly characterised by their parasitic lifestyle and the following unique morphological features: lips form a dorso-ventrally elongated perioral disc with internal sclerotizations: one midventral and two dorsosublateral (right and left); cephalic sensilla setiform, subventral sensilla are noticeably longer than the subdorsal ones; intestine extends posterior to rectum and anal opening, forming a post-anal pouch. PMID:24989765

  2. Gulosibacter molinativorax gen. nov., sp. nov., a molinate-degrading bacterium, and classification of 'Brevibacterium helvolum' DSM 20419 as Pseudoclavibacter helvolus gen. nov., sp. nov.

    PubMed

    Manaia, Célia M; Nogales, Balbina; Weiss, Norbert; Nunes, Olga C

    2004-05-01

    A Gram-positive, molinate-degrading bacterium, strain ON4(T) (=DSM 13485(T)=LMG 21909(T)), was isolated from a mixed bacterial culture able to mineralize the herbicide molinate. The strain was strictly aerobic, oxidase- and catalase-positive and non-acid-fast, with a growth temperature of 10-41 degrees C. It contained the major menaquinone MK-9 and a cell-wall peptidoglycan based on D-ornithine. 16S rDNA sequence analysis revealed that the strain formed a distinct line of descent in the family Microbacteriaceae, showing the highest 16S rDNA similarity ( approximately 95 %) to members of the genus Curtobacterium and 'Brevibacterium helvolum' DSM 20419 (=ATCC 13715). The latter was reported to have the cell-wall peptidoglycan type B2gamma and the major menaquinone MK-9, which are typical of Clavibacter, but it is clearly separated from this genus at the phylogenetic level. Based on low values of 16S rDNA sequence similarity to previously described genera and their distinctive phenotypic characteristics, it is proposed that strains ON4(T) and 'B. helvolum' DSM 20419 be classified as two novel genera and species, with the respective names Gulosibacter molinativorax gen. nov., sp. nov. and Pseudoclavibater helvolus gen. nov., sp. nov. PMID:15143025

  3. Data-Link and Surface Map Traffic Intent Displays for NextGen 4DT and Equivalent Visual Surface Operations

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Prinzel, Lawrence J., III; Arthur, Jarvis J., III; Jones, Deise R.; Allamandola, Angela S.; Bailey, Randall E.

    2009-01-01

    By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a consortium of industry, academia and government agencies have proposed a revolutionary new concept for U.S. aviation operations, termed the Next Generation Air Transportation System or "NextGen". Many key capabilities are being identified to enable NextGen, including the concept of "net-centric" operations whereby each aircraft and air services provider shares information to allow real-time adaptability to ever-changing factors such as weather, traffic, flight trajectories, and security. Data-link is likely to be the primary source of communication in NextGen. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen.

  4. Data-link and surface map traffic intent displays for NextGen 4DT and equivalent visual surface operations

    NASA Astrophysics Data System (ADS)

    Shelton, Kevin J.; Prinzel, Lawrence (Lance) J., III; Arthur, Jarvis (Trey) J., III; Jones, Denise R.; Allamandola, Angela S.; Bailey, Randall E.

    2009-05-01

    By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a consortium of industry, academia and government agencies have proposed a revolutionary new concept for U.S. aviation operations, termed the Next Generation Air Transportation System or "NextGen". Many key capabilities are being identified to enable NextGen, including the concept of "net-centric" operations whereby each aircraft and air services provider shares information to allow real-time adaptability to ever-changing factors such as weather, traffic, flight trajectories, and security. Data-link is likely to be the primary source of communication in NextGen. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen.

  5. New aerobic ammonium-dependent obligately oxalotrophic bacteria: description of Ammoniphilus oxalaticus gen. nov., sp. nov. and Ammoniphilus oxalivorans gen. nov., sp. nov.

    PubMed

    Zaitsev, G M; Tsitko, I V; Rainey, F A; Trotsenko, Y A; Uotila, J S; Stackebrandt, E; Salkinoja-Salonen, M S

    1998-01-01

    The genus Ammoniphilus is proposed for aerobic endospore-forming Gram-variable rod-shaped bacteria, which are ammonium-dependent, obligately oxalotrophic and haloalkalitolerant, oxidase- and catalase-positive, mesophilic and motile by peritrichous flagella. Cell wall contained two electron-dense layers. The external layer consists of a chain of electron-dense granules morphologically resembling the cellulosomes of Clostridium thermocellum. Two species are described, Ammoniphilus oxalaticus gen. nov., sp. nov. and Ammoniphilus oxalivorans gen. nov., sp. nov. The type strains of these species are strains RAOx-1 (= DSM 11538) and RAOx-FS (= DSM 11537), respectively. Ammoniphilus strains were isolated from the rhizosphere of sorrel (Rumex acetosa) and from decaying wood. The strains require a high concentration of ammonium ions and use oxalate as the sole organic source of carbon and energy for growth; no growth factors were required. Growth occurred at pH 6.8-9.5. The optimum temperature and pH for growth were 28-30 degrees C and 8.0-8.5. All strains grew in a saturated solution of ammonium oxalate, and tolerated 3% NaCl. Whole-cell hydrolysates contain meso-diaminopimelic acid and glucose. The menaquinone of the strains was MK 7, and the major cellular fatty acids were 12-methyl tetradecanoic, cis-hexadec-9-enoic and hexadecanoic acids. The G + C content of the DNA was 45-46 mol% for A. oxalaticus and 42 mol% for A. oxalivorans. The almost complete 16S rDNA sequence of three strains of the two species of Ammoniphilus shows that the genus falls into the radiation of the Clostridium-Bacillus subphylum of Gram-positive bacteria. The closest phylogenetic neighbour of Ammoniphilus is Oxalophagus oxalicus. The DNA-DNA hybridization value between strains RAOx-1 and RAOx-FS was 39.7%. PMID:9542085

  6. Next Gen NEAR: Near Earth Asteroid Human Robotic Precursor Mission Concept

    NASA Technical Reports Server (NTRS)

    Rivkin, Andrew S.; Kirby, Karen; Cheng, Andrew F.; Gold, Robert; Kelly, Daniel; Reed, Cheryl; Abell, Paul; Garvin, James; Landis, Rob

    2012-01-01

    Asteroids have long held the attention of the planetary science community. In particular, asteroids that evolve into orbits near that of Earth, called near-Earth objects (NEO), are of high interest as potential targets for exploration due to the relative ease (in terms of delta V) to reach them. NASA's Flexible Path calls for missions and experiments to be conducted as intermediate steps towards the eventual goal of human exploration of Mars; piloted missions to NEOs are such example. A human NEO mission is a valuable exploratory step beyond the Earth-Moon system enhancing capabilities that surpass our current experience, while also developing infrastructure for future mars exploration capabilities. To prepare for a human rendezvous with an NEO, NASA is interested in pursuing a responsible program of robotic NEO precursor missions. Next Gen NEAR is such a mission, building on the NEAR Shoemaker mission experience at the JHU/APL Space Department, to provide an affordable, low risk solution with quick data return. Next Gen NEAR proposes to make measurements needed for human exploration to asteroids: to demonstrate proximity operations, to quantify hazards for human exploration and to characterize an environment at a near-Earth asteroid representative of those that may be future human destinations. The Johns Hopkins University Applied Physics Laboratory has demonstrated exploration-driven mission feasibility by developing a versatile spacecraft design concept using conventional technologies that satisfies a set of science, exploration and mission objectives defined by a concept development team in the summer of 2010. We will describe the mission concept and spacecraft architecture in detail. Configuration options were compared with the mission goals and objectives in order to select the spacecraft design concept that provides the lowest cost, lowest implementation risk, simplest operation and the most benefit for the mission implementation. The Next Gen NEAR spacecraft was designed to support rendezvous with a range of candidate asteroid targets and could easily be launched with one of several NASA launch vehicles. The Falcon 9 launch vehicle supports a Next Gen NEAR launch to target many near-Earth asteroids under consideration that could be reached with a C3 of 18 km2/sec2 or less, and the Atlas V-401 provides added capability supporting launch to NEAs that require more lift capacity while at the same time providing such excess lift capability that another payload of opportunity could be launch in conjunction with Next Gen NEAR. Next Gen NEAR will measure and interact with the target surface in ways never undertaken at an asteroid, and will prepare for first human precursor mission by demonstrating exploration science operations at an accessible NEO. This flexible mission and spacecraft design concept supports target selection based on upcoming Earth-based observations and also provides opportunities for co-manifest & international partnerships. JHU/APL has demonstrated low cost, low risk, high impact missions and this mission will help to prepare NASA for human NEO exploration by combining the best of NASA s human and robotic exploration capabilities.

  7. GenExP, un logiciel simulateur de paysages agricoles pour l'etude de la diffusion de transg`enes

    E-print Network

    Boyer, Edmond

    dispersion des pollens et des graines d'OGM `a diff´erentes ´echelles. Abstract. The software GenExP allows or realistic field-patterns, GenExP provides multiannual maps of agricultural landscapes, which are used by softwares simulating the dispersal of GM pollen grains and seeds at various scales. Mots-cl´es. paysage

  8. NCBI Handout Series | Eukaryotic Genome Submission | Last Update March 18, 2014 Contact: info@ncbi.nlm.nih.gov Submitting Eukaryotic Genomes to GenBank

    E-print Network

    Levin, Judith G.

    NCBI Handout Series | Eukaryotic Genome Submission | Last Update March 18, 2014 Contact: info@ncbi.nlm.nih.gov Submitting Eukaryotic Genomes to GenBank Preparing eukaryotic genomes for submission to GenBank http://www.ncbi.nlm.nih.gov details are available in the online documentation: http://www.ncbi.nlm.nih.gov

  9. Enhanced Flight Vision Systems and Synthetic Vision Systems for NextGen Approach and Landing Operations

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Williams, Steven P.; Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Shelton, Kevin J.

    2013-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory standards and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility approach and landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O'Hare environment. Various scenarios tested the potential for using EFVS to conduct approach, landing, and roll-out operations in visibility as low as 1000 feet runway visual range (RVR). Also, SVS was tested to evaluate the potential for lowering decision heights (DH) on certain instrument approach procedures below what can be flown today. Expanding the portion of the visual segment in which EFVS can be used in lieu of natural vision from 100 feet above the touchdown zone elevation to touchdown and rollout in visibilities as low as 1000 feet RVR appears to be viable as touchdown performance was acceptable without any apparent workload penalties. A lower DH of 150 feet and/or possibly reduced visibility minima using SVS appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  10. Modeling Off-Nominal Recovery in NextGen Terminal-Area Operations

    NASA Technical Reports Server (NTRS)

    Callantine, Todd J.

    2011-01-01

    Robust schedule-based arrival management requires efficient recovery from off-nominal situations. This paper presents research on modeling off-nominal situations and plans for recovering from them using TRAC, a route/airspace design, fast-time simulation, and analysis tool for studying NextGen trajectory-based operations. The paper provides an overview of a schedule-based arrival-management concept and supporting controller tools, then describes TRAC implementations of methods for constructing off-nominal scenarios, generating trajectory options to meet scheduling constraints, and automatically producing recovery plans.

  11. Cetobacterium ceti gen. nov., sp. nov., a new gram-negative obligate anaerobe from sea mammals.

    PubMed

    Foster, G; Ross, H M; Naylor, R D; Collins, M D; Ramos, C P; Fernandez Garayzabal, F; Reid, R J

    1995-09-01

    Phenotypic and phylogenetic studies were performed on a Gram-negative obligately anaerobic rod-shaped bacterium isolated from two sea mammals. 16S rRNA gene sequence analysis demonstrated the bacterium represents a hitherto unknown line of descent peripherally associated to the fusobacteria and low G+C relatives. Based on the result of the phylogenetic analysis and phenotypic criteria, it is proposed that the bacterium should be assigned to a new genus, Cetobacterium ceti gen. nov., sp. nov. The type strain of Cetobacterium ceti sp. nov. is NCFB 3026. PMID:7576509

  12. Obesoconnus gen. n., a new bizarre Neotropical genus of Cyrtoscydmini (Coleoptera: Staphylinidae: Scydmaeninae).

    PubMed

    Ja?oszy?ski, Pawe?

    2014-01-01

    A new Neotropical genus of Cyrtoscydmini, Obesoconnus gen. n., is described to accommodate two new species: O. guyanensis sp. n. (the type species of Obesoconnus) from French Guyana and O. mexicanus sp. n. from Mexico. The morphology of the new taxon is described and illustrated in detail, and its possible affinities to other Cyrtoscydmini are discussed. Despite external dissimilarities, the aedeagus of Obesoconnus highly resembles copulatory organs of Alloraphes and Parastenichnaphes; all these genera share the basal pumping apparatus and apically located ostium with asymmetrical apical projections. PMID:24870336

  13. Gen IV Materials Handbook Functionalities and Operation (4A) Handbook Version 4.0

    SciTech Connect

    Ren, Weiju [ORNL

    2013-09-01

    This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

  14. Brockphasma spinifemoralis gen. et spec. nov.: a new phasmid genus and new species of Neohiraseini (Phasmida: Necrosciinae) from Vietnam.

    PubMed

    Ho, George Wai-Chun; Liu, Xing-Yue; Bresseel, Joachim; Constant, Jerome

    2014-01-01

    A new genus of stick insects, Brockphasma Ho gen. nov., with the type-species, Brockphasma spinifemoralis Ho, Liu, Bresseel & Constant spec. nov., is described and illustrated from Vietnam. Both sexes, the egg and the first instar nymph are described and figured. Data on the habitat and natural foodplants are provided. Brockphasma Ho gen. nov. is differentiated from other genera in Neohiraseini by spinose occiput, anterior region of mesonotum with a spinose hump and spinose anterodorsal and posterodorsal carinae of femora. A key to the genera of Neohiraseini from Vietnam is given. PMID:24990046

  15. Aircraft deconfliction responsibility across en-route sectors in NextGen separation assurance

    NASA Astrophysics Data System (ADS)

    Cabrall, Christopher D.

    The subject of the current research is a Next Generation Air Transportation System (NextGen) concept that involves automated separation assurance developed to enable controllers to provide both safe and efficient air traffic services at much higher traffic densities than possible today. The study investigated the issue of how responsibility should be handled between controllers for the resolution of a conflict that is predicted to occur in a sector other than where it was detected. Two possibilities, a De-Conflicting AirPlanes procedure (DCAP) versus a De-Conflicting AirSpace procedure (DCAS), were examined under human-in-the-loop simulations with scripted aircraft conflicts. Results showed that the DCAS procedure was preferred and that participants experienced less verbal coordination and took less time to resolve conflicts. The results, however, did not reveal significant differences among other plane performance metrics between DCAP and DCAS. These results indicate that the demands of NextGen separation assurance might still be met with ownership and coordination procedures (e.g., DCAP) similar to today. Reducing verbal coordination requirements, however, and allowing separation assurance responsibilities to extend more seamlessly across sector boundaries (e.g., DCAS) would evidently be more acceptable to controllers.

  16. pyGenClean: efficient tool for genetic data clean up before association testing

    PubMed Central

    Lemieux Perreault, Louis-Philippe; Provost, Sylvie; Legault, Marc-André; Barhdadi, Amina; Dubé, Marie-Pierre

    2013-01-01

    Summary: Genetic association studies making use of high-throughput genotyping arrays need to process large amounts of data in the order of millions of markers per experiment. The first step of any analysis with genotyping arrays is typically the conduct of a thorough data clean up and quality control to remove poor quality genotypes and generate metrics to inform and select individuals for downstream statistical analysis. We have developed pyGenClean, a bioinformatics tool to facilitate and standardize the genetic data clean up pipeline with genotyping array data. In conjunction with a source batch-queuing system, the tool minimizes data manipulation errors, accelerates the completion of the data clean up process and provides informative plots and metrics to guide decision making for statistical analysis. Availability and implementation: pyGenClean is an open source Python 2.7 software and is freely available, along with documentation and examples, from http://www.statgen.org. Contact: louis-philippe.lemieux.perreault@umontreal.ca or marie-pierre.dube@statgen.org PMID:23652425

  17. Flight Deck Technologies to Enable NextGen Low Visibility Surface Operations

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence (Lance) J., III; Arthur, Jarvis (Trey) J.; Kramer, Lynda J.; Norman, Robert M.; Bailey, Randall E.; Jones, Denise R.; Karwac, Jerry R., Jr.; Shelton, Kevin J.; Ellis, Kyle K. E.

    2013-01-01

    Many key capabilities are being identified to enable Next Generation Air Transportation System (NextGen), including the concept of Equivalent Visual Operations (EVO) . replicating the capacity and safety of today.s visual flight rules (VFR) in all-weather conditions. NASA is striving to develop the technologies and knowledge to enable EVO and to extend EVO towards a Better-Than-Visual operational concept. This operational concept envisions an .equivalent visual. paradigm where an electronic means provides sufficient visual references of the external world and other required flight references on flight deck displays that enable Visual Flight Rules (VFR)-like operational tempos while maintaining and improving safety of VFR while using VFR-like procedures in all-weather conditions. The Langley Research Center (LaRC) has recently completed preliminary research on flight deck technologies for low visibility surface operations. The work assessed the potential of enhanced vision and airport moving map displays to achieve equivalent levels of safety and performance to existing low visibility operational requirements. The work has the potential to better enable NextGen by perhaps providing an operational credit for conducting safe low visibility surface operations by use of the flight deck technologies.

  18. Distribution of Hammerhead and Hammerhead-like RNA Motifs Through the GenBank

    PubMed Central

    Ferbeyre, Gerardo; Bourdeau, Véronique; Pageau, Marie; Miramontes, Pedro; Cedergren, Robert

    2000-01-01

    Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive DNA from certain species of newts and schistosomes. To determine if this catalytic RNA motif has a wider distribution, we decided to scrutinize the GenBank database for RNAs that contain hammerhead or hammerhead-like motifs. The search shows a widespread distribution of this kind of RNA motif in different sequences suggesting that they might have a more general role in RNA biology. The frequency of the hammerhead motif is half of that expected from a random distribution, but this fact comes from the low CpG representation in vertebrate sequences and the bias of the GenBank for those sequences. Intriguing motifs include those found in several families of repetitive sequences, in the satellite RNA from the carrot red leaf luteovirus, in plant viruses like the spinach latent virus and the elm mottle virus, in animal viruses like the hepatitis E virus and the caprine encephalitis virus, and in mRNAs such as those coding for cytochrome P450 oxidoreductase in the rat and the hamster. PMID:10899150

  19. Advanced Technology Development Program for Lithium-Ion Batteries: Gen 2 Performance Evaluation Final Report

    SciTech Connect

    Jon P. Christophersen; Ira Bloom; Edward V. Thomas; Kevin L. Gering; Gary L. Henriksen; Vincent S. Battaglia; David Howell

    2006-07-01

    The Advanced Technology Development Program has completed performance testing of the second generation of lithium-ion cells (i.e., Gen 2 cells). The 18650-size Gen 2 cells, with a baseline and variant chemistry, were distributed over a matrix consisting of three states-of-charge (SOCs) (60, 80, and 100% SOC), four temperatures (25, 35, 45, and 55°C), and three life tests (calendar-, cycle-, and accelerated-life). The calendar- and accelerated-life cells were clamped at an open-circuit voltage corresponding to the designated SOC and were subjected to a once-per-day pulse profile. The cycle-life cells were continuously pulsed using a profile that was centered around 60% SOC. Life testing was interrupted every four weeks for reference performance tests (RPTs), which were used to quantify changes in cell degradation as a function of aging. The RPTs generally consisted of C1/1 and C1/25 static capacity tests, a low-current hybrid pulse power characterization test, and electrochemical impedance spectroscopy. The rate of cell degradation generally increased with increasing test temperature, and SOC. It was also usually slowest for the calendar-life cells and fastest for the accelerated-life cells. Detailed capacity-, power-, and impedance-based performance results are reported.

  20. Two new species of Pharta Thorell, 1891 with the description of Ibana senagang gen. et sp. nov. (Araneae: Thomisidae).

    PubMed

    Benjamin, Suresh P

    2014-01-01

    Two new species of Pharta, P. sudmannorum sp. nov. (??, Borneo) and P. koponeni sp. nov. (?, Thailand) are described. Furthermore, Ibana senagang gen. nov. & sp. nov. from Malaysia is described based on its exceptional palp, which has a reduced, movable conductor and thick-long spines on the distal, ventral surface of the tibia, reminiscent of Epidius Thorell, 1877. PMID:25544630

  1. YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps.

    PubMed

    Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S; Liang, Chun

    2014-01-01

    Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory). PMID:25009553

  2. CONCURRENT SESSION I--Wildland Ecosystem Topics 48 USDA Forest Service Gen. Tech. Rep. PSW-GTR-158. 1995.

    E-print Network

    Standiford, Richard B.

    CONCURRENT SESSION I--Wildland Ecosystem Topics #12;48 USDA Forest Service Gen. Tech. Rep. PSW Symposium: Fire Issues and Solutions in Urban Interface and Wildland Ecosystems, February 15-17, 1994, Walnut Creek, California. 2Prescribed Fire Specialist, Western Region, USDI National Park Ser- vice, 600

  3. OmniGen-AF supplementation modulated the physiological and acute phase responses of Brahman heifers to an endotoxin challenge

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study examined the effect of feeding OmniGen-AF (OG; Prince Agri Products) on the physiological and acute phase responses (APR) of newly-weaned heifers to an endotoxin (lipopolysaccharide; LPS) challenge. Brahman heifers (n=24; 183±5 kilograms) from the Texas AgriLife Research Center in Overton...

  4. Modulation of the metabolic response to an endotoxin challenge in Brahman heifers through OmniGen-AF supplementation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study examined the effect of feeding OmniGen-AF (OG; Prince Agri Products) on the metabolic response of newly-weaned heifers to an endotoxin (lipopolysaccharide; LPS) challenge. Brahman heifers (n=24; 183±5 kilograms) from the Texas AgriLife Research Center in Overton, TX, were separated into 2...

  5. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 467 Standing Dead Tree Dynamics Extracted

    E-print Network

    Standiford, Richard B.

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 467 Standing Dead Tree Dynamics Extracted provide valuable information on standing dead tree dynamics. Even if dead trees were not traditionally measured, a subsequent measurement of dead trees enables extraction of information on past dynamics

  6. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 85 How Much Dead Wood in Stream Channels

    E-print Network

    Standiford, Richard B.

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 85 How Much Dead Wood in Stream Channels Is Enough?1 Thomas E. Lisle2 Abstract Private forest managers often seek guidelines on how much dead wood an understanding of ecologic functions of dead wood in streams to determine the amount needed to fulfill ecologic

  7. 109USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Patterns and Processes of Adaptation

    E-print Network

    Standiford, Richard B.

    109USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Patterns and Processes of Adaptation suggest local scale adaptation. Differences among maternal families in survival and growth were that natural selection has resulted in the formation of genetically differentiated populations adapted to local

  8. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 33 breed on the Farallon Islands in the Pacific Ocean (Common

    E-print Network

    Standiford, Richard B.

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 33 breed on the Farallon Islands in the Pacific Ocean (Common Murre, Pigeon Guillemot, Cassin's Auklet, Rhinoceros Auklet, and Tufted Puffin fish feeding alcids of the northern Pacific Ocean (Kittlitz's Murrelet, Pigeon Guillemot, Spectacled

  9. What happens when someone talks in public to an audience they know to be entirely computer gen-

    E-print Network

    Slater, Mel

    designed a virtual public speaking scenario, followed by an experimental study. In this work we wanted compared to more general social interactions. A public speaking scenario involves specific stylizedWhat happens when someone talks in public to an audience they know to be entirely computer gen

  10. 527USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Improved Methods to Evaluate the

    E-print Network

    Standiford, Richard B.

    527USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Improved Methods to Evaluate the Impact: This study includes a review of scientific and planning literature, interviews with practicing wildlife methods for the assessment of wildlife populations and biological diversity where subdivisions have been

  11. JENUFA GEN. NOV.: A NEW GENUS OF COCCOID GREEN ALGAE (CHLOROPHYCEAE, INCERTAE SEDIS) PREVIOUSLY RECORDED BY ENVIRONMENTAL SEQUENCING1

    E-print Network

    JENUFA GEN. NOV.: A NEW GENUS OF COCCOID GREEN ALGAE (CHLOROPHYCEAE, INCERTAE SEDIS) PREVIOUSLY of unicellular green algae from algal biofilms growing on tree bark in a Southeast Asian tropical rainforest: AU, approximately unbiased; BBM, Bold basal medium; CAUP, Culture Collection of algae at Charles

  12. 169USDAForestServiceGen.Tech.Rep.PSW-GTR-160.1997. Growth of Blue Oak on California's

    E-print Network

    Standiford, Richard B.

    have an understory of annual grasses and occasional native perennial grasses, and are found169USDAForestServiceGen.Tech.Rep.PSW-GTR-160.1997. Growth of Blue Oak on California's Hardwood Rangelands1 Richard B. Standiford2 Abstract. An individual tree basal area increment model was developed

  13. Gen Green: Changes in Australian Apprentices' and Trainees' Experience of Skills and Sustainability from 2008 to 2011

    ERIC Educational Resources Information Center

    Sack, Fabian

    2012-01-01

    The Gen Green research in 2008 and 2011 indicates that skills for sustainability public policy and business initiatives are having an impact, but that young skilled Australians' high level of interest in sustainability skills is confounded by a lack of guidance and incentives from employers, the market and educators. The research indicates that,…

  14. 1.Phys. A: Math. Gen. 27 (1994) 2687-2708. Printed in the UK On the 3D Isingspin glass

    E-print Network

    Ritort, Felix

    1994-01-01

    1.Phys. A: Math. Gen. 27 (1994) 2687-2708. Printed in the UK On the 3D Isingspin glass Enzo, 08028 Barcelona. Spain Received 21 October 1993 Abstract We study the 3D king spin glass with i l look at the history of the subject is useful. If we look at the period that begins when people first

  15. 65USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Soil Characteristics of Blue Oak and

    E-print Network

    Standiford, Richard B.

    65USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Soil Characteristics of Blue Oak and Coast, California, soils associated with blue oaks (Quercus douglasii) are slightly more acidic, have finer textures are richer in organic matter than those associated with blue oaks. Blue oaks seem to grow more frequently

  16. Arch Gen Psychiatry . Author manuscript Impact of smoking on cognitive decline in early old age: the Whitehall II

    E-print Network

    lifespan of smokers. Objective To examine the association between smoking history and cognitive decline the entire study period. Linear mixed models were used to assess the association between smoking historyArch Gen Psychiatry . Author manuscript Page /1 12 Impact of smoking on cognitive decline in early

  17. Morphology and phylogenetic relationships of the neotenic interstitial polychaete Apodotrocha progenerans n.gen., n.sp. (Annelida)

    Microsoft Academic Search

    W. Westheide; N. W. Riser

    1983-01-01

    Apodotrocha progenerans n.gen., n.sp. from tidal beaches or shallow waters on the east coast of the USA (Massachusetts) is a gonochoristic interstitial polychaete (length ca. 600 µm; six trunk segments), that lacks parapods, setae, and fleshy appendages, but has three characteristic caudal cirri. The habitus greatly resembles a larval stage of the Dorvilleidae, a family with which it also shares

  18. USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 167 Biodiversity in the Sierra Nevada1

    E-print Network

    Standiford, Richard B.

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-193. 2004. 167 Biodiversity in the Sierra Nevada1's wealth of biodiversity was appreciated fully and documented in earnest. Indeed, by the time naturalists, composition, and distribution of the native biodiversity of the Sierra Nevada prior to European

  19. USDA Forest Service Gen. Tech. Rep. PSW-GTR-203. 2007. 41 Stewardship and Fireshed Assessment: A

    E-print Network

    Standiford, Richard B.

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-203. 2007. 41 Stewardship and Fireshed Assessment where funding provides the most benefits. Stewardship and Fireshed Assessment (SFA National Forest, USDA Forest Service, on detail to the Stewardship and Fireshed Assessment Cadre. #12

  20. 120 USDA Forest Service Gen. Tech. Rep. RMRS-GTR-98. 2002 Abies amabilis 45, 50, 54, 59, 60

    E-print Network

    durangensis 33, 45 Abies grandis 45, 49, 50, 54, 59 Abies lasiocarpa 45, 46, 54, 59, 60 Abies lasiocarpa var120 USDA Forest Service Gen. Tech. Rep. RMRS-GTR-98. 2002 A Abies 29 Abies amabilis 45, 50, 54, 59, 60 Abies balsamea 57 Abies bifolia 45, 50 Abies concolor 4, 26, 31, 32, 45, 49, 50, 70, 92 Abies

  1. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 621 Assessing the Effect of Fire Regime on

    E-print Network

    Standiford, Richard B.

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 621 Assessing the Effect of Fire Regime as high in landscapes having an infrequent, stand-replacing fire regime (173 Mg/ha) as in landscapes stand. CWD is therefore highest just after such a fire. This material persists as the regenerating stand

  2. 347USDA Forest Service Gen.Tech. Rep. PSW-GTR-160. 1997. Influence of Supplemental Feeding

    E-print Network

    Standiford, Richard B.

    347USDA Forest Service Gen.Tech. Rep. PSW-GTR-160. 1997. Influence of Supplemental Feeding Sites these areas and into areas where high amounts of RDM were consistently left in the fall, the amount of cattle 1988). Residual dry matter is the dry plant material left on the ground from the current year's forage

  3. 445USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. An Examination of the OakWoodland

    E-print Network

    Standiford, Richard B.

    445USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. An Examination of the Oak hardwood lumber industry revealed a fragmented industry with many sole proprietorships and a raw-material properties and the experience of local artisans and woodworkers, successful markets for high-value wood

  4. 457USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. California Black Oak--From Firewood

    E-print Network

    Standiford, Richard B.

    457USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. California Black Oak--From Firewood have traditionally been sold for firewood, but a better economic use of this material would, an underutilization of its economic potential. The High Sierra Resource Conservation and Development Area Council

  5. Gen Relativ Gravit (2006) 38:13291330 DOI 10.1007/s10714-006-0313-2

    E-print Network

    Krasinski, Andrzej

    2006-01-01

    by J. T. Jebsen reprinted in Gen. Rel. Grav. 37, 2253 ­ 2259 (2005) J. Ehlers · A. Krasi´nski Published online: 18 July 2006 © Springer-Verlag 2006 Jebsen [1] anticipated Birkhoff [2] in claimingSitter and Anti-DS. The mistake in the proof occurs where Jebsen claims that in a spherically symmetric metric ds2

  6. 204 USDA Forest Service Gen. Tech. Rep. RMRS-GTR-114. 2003 Part 3: Soil Properties, Erosion,

    E-print Network

    204 USDA Forest Service Gen. Tech. Rep. RMRS-GTR-114. 2003 Part 3: Soil Properties, Erosion, erosion and sedimentation, and how aquatic and terrestrial ecosystems have responded or could respond erosion/sedimentation events (re- lated to fire or other processes); how did the frequency, extent

  7. Dorinnotheca streelii Fairon-Demaret, gen. et sp. nov., a new early seed plant from the upper Famennian of Belgium

    Microsoft Academic Search

    Muriel Fairon-Demaret

    1996-01-01

    Dorinnotheca streelii Fairon-Demaret, gen. et sp. nov. is described from three upper Famennian localities in Belgium. This new early seed plant bears cupules hanging singly at the tips of the slender ultimate axes of a pinnately branched system. Each cupule encloses a single, centrally located preovule with four free integumentary lobes. At the base of the fertile unit, the cupule

  8. PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees

    Microsoft Academic Search

    Andrew Rambaut; J. Adachi

    1997-01-01

    Motivation: Seq-Gen is a program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. Nucleotide frequencies and other parameters of the model may be given and site-specific rate heterogeneity can also be incorporated in a number of

  9. GenLab: A MATLAB ®-based program for structural analysis of folds mapped by GPS or seismic methods

    Microsoft Academic Search

    J. L. Fernández-Martínez; Richard J. Lisle

    2009-01-01

    GenLab is a MATLAB® code for structural analysis of digitally and seismically mapped horizons based on the geometrical model of the developable surface. This model is chosen because surfaces of this type result from the bending of a non-stretching stratum and because deviation from developable geometry implies that bed stretching during folding has occurred. The model is therefore linked with

  10. USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 83 Breeding and Natal Dispersal, Nest Habitat Loss and

    E-print Network

    Standiford, Richard B.

    USDA Forest Service Gen. Tech. Rep. PSW-152. 1995. 83 Breeding and Natal Dispersal, Nest Habitat 95825 Abstract: Evidence of breeding and natal dispersal in alcids is typically provided in consecutive breeding seasons, breeding site fidelity (birds breeding in the same nest as the previous year

  11. USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 593 Dead Branches and Other Wildlife

    E-print Network

    Standiford, Richard B.

    USDA Forest Service Gen. Tech. Rep. PSW-GTR-181. 2002. 593 Dead Branches and Other Wildlife,4 and Matthew L. Triggs5 Abstract In 1995, we began counting dead branches, mistletoe, and acorns on individually tagged living California black oak (Quercus kelloggii). On the same plots, data on dead branches

  12. 267USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Rehabilitation of a Blue Oak

    E-print Network

    Standiford, Richard B.

    267USDA Forest Service Gen. Tech. Rep. PSW-GTR-160. 1997. Rehabilitation of a Blue Oak Restoration. Results indicate treeshelters release stunted seedlings and could rehabilitate poorly performing projects attempted to rehabilitate our original planting, in order to evaluate readily available measures applicable

  13. Roseimicrobium gellanilyticum gen. nov., sp. nov., a new member of the class Verrucomicrobiae.

    PubMed

    Otsuka, Shigeto; Ueda, Hiroyuki; Suenaga, Taku; Uchino, Yoshihito; Hamada, Moriyuki; Yokota, Akira; Senoo, Keishi

    2013-06-01

    The taxonomic properties of strain DC2a-G7(T), a Gram-negative, ovoid to rod-shaped, gellan gum-lysing bacterium, were examined. The 16S rRNA gene sequence similarity showed that DC2a-G7(T) is a member of the phylum Verrucomicrobia and the closest type strain of a species with a validly published name is Verrucomicrobium spinosum DSM 4136(T), with a sequence similarity of 91.2%. In addition to this similarity value lower than 95%, the absence of prostheca, the orangey-red colony colour and the compositions of the major menaquinones and polar lipids also supported the differentiation of this bacterium from the genus Verrucomicrobium. Here, we propose the name Roseimicrobium gellanilyticum gen. nov., sp. nov. for the isolate. The type strain of Roseimicrobium gellanilyticum is DC2a-G7(T) (=NBRC 108606(T)=DSM 25532(T)). PMID:23041636

  14. Brevifollis gellanilyticus gen. nov., sp. nov., a gellan-gum-degrading bacterium of the phylum Verrucomicrobia.

    PubMed

    Otsuka, Shigeto; Suenaga, Taku; Vu, Hoan Thi; Ueda, Hiroyuki; Yokota, Akira; Senoo, Keishi

    2013-08-01

    The taxonomic properties of strain DC2c-G4(T), a Gram-staining-negative, ovoid, gellan-gum-degrading bacterial isolate, were examined. Phylogenetic analysis based on 16S rRNA gene sequences identified this isolate as a member of the phylum Verrucomicrobia and closest to the genus Prosthecobacter. The 16S rRNA gene sequence similarities between this isolate and any of the type strains of species of the genus Prosthecobacter were less than 95 %. In addition, the absence of a single prostheca and the predominant menaquinone MK-7(H2) supported the differentiation of this isolate from the genus Prosthecobacter. Here, we propose Brevifollis gellanilyticus gen. nov., sp. nov. to accommodate the isolate. The type strain of the type species is DC2c-G4(T) (= NBRC 108608(T) = CIP 110457(T)). PMID:23416572

  15. PubCrawler: keeping up comfortably with PubMed and GenBank.

    PubMed

    Hokamp, Karsten; Wolfe, Kenneth H

    2004-07-01

    The free PubCrawler web service (http://www.pubcrawler.ie) has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short notifications or emails with the latest updates as soon as they become available. A new output format and more flexibility for the email formatting help PubCrawler cope with increasing challenges arising from browser incompatibilities and mail filters, therefore making it suitable for a wide range of users. PMID:15215341

  16. IceCube-Gen2: A Vision for the Future of Neutrino Astronomy in Antarctica

    E-print Network

    Aartsen, M G; Adams, J; Aguilar, J A; Ahlers, M; Ahrens, M; Altmann, D; Anderson, T; Anton, G; Arguelles, C; Arlen, T C; Auffenberg, J; Axani, S; Bai, X; Bartos, I; Barwick, S W; Baum, V; Bay, R; Beatty, J J; Tjus, J Becker; Becker, K -H; BenZvi, S; Berghaus, P; Berley, D; Bernardini, E; Bernhard, A; Besson, D Z; Binder, G; Bindig, D; Bissok, M; Blaufuss, E; Blumenthal, J; Boersma, D J; Bohm, C; Bos, F; Bose, D; Böser, S; Botner, O; Brayeur, L; Bretz, H -P; Brown, A M; Buzinsky, N; Casey, J; Casier, M; Cheung, E; Chirkin, D; Christov, A; Christy, B; Clark, K; Classen, L; Clevermann, F; Coenders, S; Collin, G H; Conrad, J M; Cowen, D F; Silva, A H Cruz; Daughhetee, J; Davis, J C; Day, M; de André, J P A M; De Clercq, C; De Ridder, S; Desiati, P; de Vries, K D; de With, M; DeYoung, T; andaz-Vélez, J C Dí; Dunkman, M; Eagan, R; Eberhardt, B; Ehrhardt, T; Eichmann, B; Eisch, J; Euler, S; Evans, J J; Evenson, P A; Fadiran, O; Fazely, A R; Fedynitch, A; Feintzeig, J; Felde, J; Filimonov, K; Finley, C; Fischer-Wasels, T; Flis, S; Frantzen, K; Fuchs, T; Gaisser, T K; Gaior, R; Gallagher, J; Gerhardt, L; Gier, D; Gladstone, L; Glüsenkamp, T; Goldschmidt, A; Golup, G; Gonzalez, J G; Goodman, J A; Góra, D; Grant, D; Gretskov, P; Groh, J C; Groß, A; Ha, C; Haack, C; Ismail, A Haj; Hallen, P; Hallgren, A; Halzen, F; Hanson, K; Haugen, J; Hebecker, D; Heereman, D; Heinen, D; Helbing, K; Hellauer, R; Hellwig, D; Hickford, S; Hignight, J; Hill, G C; Hoffman, K D; Hoffmann, R; Homeier, A; Hoshina, K; Huang, F; Huelsnitz, W; Hulth, P O; Hultqvist, K; Ishihara, A; Jacobi, E; Jacobsen, J; Japaridze, G S; Jero, K; Jlelati, O; Jones, B J P; Jurkovic, M; Kalekin, O; Kappes, A; Karg, T; Karle, A; Katori, T; Katz, U F; Kauer, M; Keivani, A; Kelley, J L; Kheirandish, A; Kiryluk, J; Kläs, J; Klein, S R; Köhne, J -H; Kohnen, G; Kolanoski, H; Koob, A; Köpke, L; Kopper, C; Kopper, S; Koskinen, D J; Kowalski, M; Krauss, C B; Kriesten, A; Krings, K; Kroll, G; Kroll, M; Kunnen, J; Kurahashi, N; Kuwabara, T; Labare, M; Lanfranchi, J L; Larsen, D T; Larson, M J; Lesiak-Bzdak, M; Leuermann, M; LoSecco, J; Lünemann, J; Madsen, J; Maggi, G; Mahn, K B M; Marka, S; Marka, Z; Maruyama, R; Mase, K; Matis, H S; Maunu, R; McNally, F; Meagher, K; Medici, M; Meli, A; Meures, T; Miarecki, S; Middell, E; Middlemas, E; Milke, N; Miller, J; Mohrmann, L; Montaruli, T; Moore, R W; Morse, R; Nahnhauer, R; Naumann, U; Niederhausen, H; Nowicki, S C; Nygren, D R; Obertacke, A; Odrowski, S; Olivas, A; Omairat, A; O'Murchadha, A; Palczewski, T; Paul, L; Penek, Ö; Pepper, J A; Heros, C Pérez de los; Pfendner, C; Pieloth, D; Pinat, E; Pinfold, J L; Posselt, J; Price, P B; Przybylski, G T; Pütz, J; Quinnan, M; Rädel, L; Rameez, M; Rawlins, K; Redl, P; Rees, I; Reimann, R; Relich, M; Resconi, E; Rhode, W; Richman, M; Riedel, B; Robertson, S; Rodrigues, J P; Rongen, M; Rott, C; Ruhe, T; Ruzybayev, B; Ryckbosch, D; Saba, S M; Sander, H -G; Sandroos, J; Sandstrom, P; Santander, M; Sarkar, S; Schatto, K; Scheriau, F; Schmidt, T; Schmitz, M; Schoenen, S; Schöneberg, S; Schönwald, A; Schukraft, A; Schulte, L; Schulz, O; Seckel, D; Sestayo, Y; Seunarine, S; Shaevitz, M H; Shanidze, R; Smith, M W E; Soldin, D; Söldner-Rembold, S; Spiczak, G M; Spiering, C; Stamatikos, M; Stanev, T; Stanisha, N A; Stasik, A; Stezelberger, T; Stokstad, R G; andl, A Stöß; Strahler, E A; Ström, R; Strotjohann, N L; Sullivan, G W; Taavola, H; Taboada, I; Taketa, A; Tamburro, A; Tepe, A; Ter-Antonyan, S; Terliuk, A; Teš, G; andi?,; Tilav, S; Toale, P A; Tobin, M N; Tosi, D; Tselengidou, M; Unger, E; Usner, M; Vallecorsa, S; van Eijndhoven, N; Vandenbroucke, J; van Santen, J; Vanheule, S; Vehring, M; Voge, M; Vraeghe, M; Walck, C; Wallraff, M; Weaver, Ch; Wellons, M; Wendt, C; Westerhoff, S; Whelan, B J; Whitehorn, N; Wichary, C; Wiebe, K; Wiebusch, C H; Williams, D R; Wissing, H; Wolf, M; Wood, T R; Woschnagg, K; Wren, S; Xu, D L; Xu, X W; Xu, Y; Yanez, J P; Yodh, G; Yoshida, S; Zarzhitsky, P; Ziemann, J; Zoll, M

    2014-01-01

    The recent observation by the IceCube neutrino observatory of an astrophysical flux of neutrinos represents the "first light" in the nascent field of neutrino astronomy. The observed diffuse neutrino flux seems to suggest a much larger level of hadronic activity in the non-thermal universe than previously thought and suggests a rich discovery potential for a larger neutrino observatory. This document presents a vision for an substantial expansion of the current IceCube detector, IceCube-Gen2, including the aim of instrumenting a $10\\,\\mathrm{km}^3$ volume of clear glacial ice at the South Pole to deliver substantial increases in the astrophysical neutrino sample for all flavors. A detector of this size would have a rich physics program with the goal to resolve the sources of these astrophysical neutrinos, discover GZK neutrinos, and be a leading observatory in future multi-messenger astronomy programs.

  17. NASA System-Level Design, Analysis and Simulation Tools Research on NextGen

    NASA Technical Reports Server (NTRS)

    Bardina, Jorge

    2011-01-01

    A review of the research accomplished in 2009 in the System-Level Design, Analysis and Simulation Tools (SLDAST) of the NASA's Airspace Systems Program is presented. This research thrust focuses on the integrated system-level assessment of component level innovations, concepts and technologies of the Next Generation Air Traffic System (NextGen) under research in the ASP program to enable the development of revolutionary improvements and modernization of the National Airspace System. The review includes the accomplishments on baseline research and the advancements on design studies and system-level assessment, including the cluster analysis as an annualization standard of the air traffic in the U.S. National Airspace, and the ACES-Air MIDAS integration for human-in-the-loop analyzes within the NAS air traffic simulation.

  18. Multimodal information Management: Evaluation of Auditory and Haptic Cues for NextGen Communication Displays

    NASA Technical Reports Server (NTRS)

    Begault, Durand R.; Bittner, Rachel M.; Anderson, Mark R.

    2012-01-01

    Auditory communication displays within the NextGen data link system may use multiple synthetic speech messages replacing traditional ATC and company communications. The design of an interface for selecting amongst multiple incoming messages can impact both performance (time to select, audit and release a message) and preference. Two design factors were evaluated: physical pressure-sensitive switches versus flat panel "virtual switches", and the presence or absence of auditory feedback from switch contact. Performance with stimuli using physical switches was 1.2 s faster than virtual switches (2.0 s vs. 3.2 s); auditory feedback provided a 0.54 s performance advantage (2.33 s vs. 2.87 s). There was no interaction between these variables. Preference data were highly correlated with performance.

  19. Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil.

    PubMed

    Guo, Lin; Tuo, Li; Habden, Xugela; Zhang, Yuqin; Liu, Jiameng; Jiang, Zhongke; Liu, Shaowei; Dilbar, Tohty; Sun, Chenghang

    2015-01-01

    A novel actinomycete, designated strain CA15-2(T), was isolated from a soil sample collected from the rhizosphere of tamarisk in the Lop Nor region, Xinjiang, China, and was characterized by using a polyphasic taxonomic approach. Optimal growth occurred at 37 °C and pH 7.5-8.0 and with 5% (w/v) NaCl. Strain CA15-2(T) formed white to pale-yellow branched substrate mycelium without fragmentation and sparse aerial mycelium with wavelike curves. Whole-cell hydrolysates of the isolate contained meso-diaminopimelic acid as the diagnostic diamino acid of the cell wall but no diagnostic sugars. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylethanolamine, one unidentified glycolipid, one unidentified phospholipid and other unidentified lipids. MK-9(H8), MK-10(H8) and MK-10(H6) were the predominant menaquinones. The major fatty acids were iso-C16:0 and C16:0. The G+C content of the genomic DNA was 69.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CA15-2(T) formed a distinct subclade in the family Nocardiopsaceae, with less than 95% 16S rRNA gene sequence similarity to all known members of the family Nocardiopsaceae. On the basis of the evidence from our polyphasic study, a novel genus, Allosalinactinospora gen. nov., is proposed, with the type species Allosalinactinospora lopnorensis gen. nov., sp. nov. The type strain of Allosalinactinospora lopnorensis is strain CA15-2(T) (?=?DSM 45697(T)?=CGMCC 4.7074(T)). PMID:25332211

  20. Digyalum oweni, gen. nov., sp. nov., a new and unusual gregarin protozoan from the gut of mollusc Littorina obtusata (Prosobranchia: Gastropoda).

    PubMed

    Koura, E A; Grahame, J; Owen, R W; Kamel, E G

    1990-06-01

    Digyalum oweni, gen. nov., sp. nov., is described from the gut of the gastropod mollusc Littorina obtusata. The gregarine has the unusual features of transverse orientation of the epicyte folds and two anterior pouch-like hollows. PMID:2110230

  1. GenBank at Los Alamos: User manual, training guide, and reference manual for the OPEN LOOK[trademark] AWB

    SciTech Connect

    Reese, G.C.; Keen, G.M.; Gilna, P.; Cinkosky, M.J.

    1993-03-15

    The GenBank project at Los Alamos collects nucleotide sequence submissions from the biological research community. This work includes the processing of data received in several different forms as well as maintenance and quality control on those submissions. This manual explains the procedures involved in that work for both Los Alamos GenBank staff and off-site users. The GenBank database stores annotated DNA sequences. This manual contains the procedures for depositing these sequences into the database. There are two ways to do this. Either the sequence arrives at GenBank as a submission and is entered by the database staff or the sequence is directly entered by an off-site user. The Annotator's WorkBench (AWB), which is a database browsing and editing tool, is used in both cases. This manual is for GenBank staff and off-site users of the GenBank database at the Los Alamos National Laboratory. It contains an introduction and tutorials for AWB, as well as procedures for entering sequences either as submissions or as data directly deposited by an off-site user. Instructions for all of these are found in Chapters 2 through 4. The introduction to AWB is in Chapter 2. Instructions for submission handling are in Chapter 3. Instructions for entering sequence information are in Chapter 4. Off-site users should look at section 4.3 for instructions on entering a sequence. In addition, the manual describes various in-house curatorial tasks that are part of maintaining the database, as well as the procedures and conventions for annotating sequences. The procedures for annotation and review are in Chapters 5 and 6. The description of in-house curator's tasks is in Chapter 7. The appendices contain: Annotation conventions, two reference chapters on AWB and other utility programs, a complete list of all the forms, fields, and commands in AWB and descriptions of other (non-AWB) software utilities used by database staff.

  2. Koponenius gen. nov., a new genus of the millipede family Haplodesmidae from the Himalayas of India and Nepal (Diplopoda: Polydesmida).

    PubMed

    Golovatch, Sergei I; Vandenspiegel, Didier

    2014-01-01

    The first, apparently westernmost indigenous representatives of Haplodesmidae are reported, from the Himalayas of Nepal and India. Both new species belong to a new genus, Koponenius gen. nov., with K. unicornis sp. nov., the type species from Darjeeling District, NE India, and K. biramus sp. nov., from Nepal. The new genus is superficially very similar to Prosopodesmus Silvestri, 1910, most species of which seem to be native to tropical Australia, partly also to southern Japan. However, Koponenius gen. nov. is easily distinguished in showing only 19 body segments, a special ozopore formula (5, 7-18), 4 transverse rows of setigerous isostictic tubercles per postcollum metatergum, and a clearly helicoid, twisted prefemoral portion of the gonopod so that the seminal groove runs mostly laterally, not mesally.  PMID:25544626

  3. NexGen LPS rotating platform total knee arthroplasty: medium-term results of a prospective study

    Microsoft Academic Search

    Roberto Rossi; Andrea Ferro; Matteo Bruzzone; Davide Edoardo Bonasia; Giacomo Garzaro; Filippo Castoldi

    2009-01-01

    The purpose of this study is to present midterm results of NexGen LPS (Zimmer, Warsaw) rotating platform total knee arthroplasty.\\u000a A prospective consecutive series of 50 primary rotating platform total knee replacements in 43 patients were clinically and\\u000a radiographically evaluated at a mean follow-up of 46.4 (range 30–78) months. There were 12 men (30%) and 31 women (70%) with\\u000a an

  4. Human-in-the-Loop Evaluation of Ground-Based Automated Separation Assurance for NextGen

    Microsoft Academic Search

    Thomas Prevot; Jeffrey Homola; Joey Mercer

    2008-01-01

    Summary This paper describes human-in-the-loop research at NASA Ames Research Center on service provider-based automated separation assurance for the Next Generation Air Transportation System (NextGen). Key human\\/automation integration aspects such as levels of automation and roles and responsibilities of automated separation management are investigated in the Airspace Operations Laboratory. A trilogy of part-task studies was designed to examine efficiency, safety,

  5. Praecocilenchus rhaphidophorus n. gen., n. sp. (Nematoda: Aphelenchoidea) Parasitizing Rhynchophorus bilineatus (Montrouzier) (Coleoptera: Curculionidae) in New Britain

    PubMed Central

    Poinar, G. O.

    1969-01-01

    Praecocilenchus rhaphidophorus n. gen., n. sp. is described as a new endoparasitic aphelenchoid nematode parasitizing adults of the palm weevil, Rhynchophorus bilineatus (Montrouzier). P. rhaphidophorus is unusual in that juveniles develop to maturity within the female uterus and thin, needle-shaped crystals form in the intestines of mature parasitic females. Hundreds of parasitic female nematodes were found in the body cavity of infected hosts. The role of this parasite as a biological control agent of Rhynchophorus weevils is discussed. PMID:19325682

  6. Osornodella gabrielae, n. gen. and n. sp., a new falklandellid (Amphipoda: Gammaridea) from freshwaters of the Chilean Coastal Range.

    PubMed

    Pérez-Schultheiss, Jorge

    2013-01-01

    The first species of falklandellid amphipod outside the Falkland Islands: Osornodella gabrielae n. gen., n. sp. is described from freshwaters of subterranean origin in the Coastal Range of Osorno province, Chile. The new taxon is characterized principally by the absence of secondary sexual characters in pereopods 3-4, uropod 3 aequiramous and telson slightly cleft. The new species is described and illustrated and its morphological relationships with other known species of this group are discussed. PMID:24613998

  7. Integrating Instruction, Assessment, & Evaluation in a Technology Based Genetics Environment: The GenScope™ Follow-up Study

    Microsoft Academic Search

    Daniel T. Hickey; Ann C. H. Kindfield

    2000-01-01

    A previously reported study in 24 secondary science classrooms showed the GenScope computer-supported learning environment to be at least as effective as conventional curricula at enhancing genetics reasoning ability. A follow-up study in three more classrooms yielded the dramatic reasoning gains we had been seeking, partly by addressing four unresolved issues from the prior research. First, addressing previous difficulties implementing

  8. A new fungicolous Scolecobasidium (hyphomycetes) and Caducirostrum gen. nov. (coelomycetes) from leaf litter in the UK and Italy

    Microsoft Academic Search

    E. Punithalingam; Brian M. Spooner

    Summary  Two new microfungi, a fungicolous Scolecobasidium, S. rostricola sp. nov., colonising the ostiolar necks of a new coelomycete, Caducirostrum foliicola gen. & sp. nov., on leaf litter of Viburnum tinus, Arbutus unedo,\\u000a Prunus laurocerasus and P. lusitanica from the U.K. and Italy, are described, illustrated and compared with other relevant taxa. Rhabdostromina, with new combinations for Dendroseptoria arrhenatheri and D.

  9. Meeting Air Transportation Demand in 2025 by Using Larger Aircraft and Alternative Routing to Complement NextGen Operational Improvements

    NASA Technical Reports Server (NTRS)

    Smith, Jeremy C.; Guerreiro, Nelson M.; Viken, Jeffrey K.; Dollyhigh, Samuel M.; Fenbert, James W.

    2010-01-01

    A study was performed that investigates the use of larger aircraft and alternative routing to complement the capacity benefits expected from the Next Generation Air Transportation System (NextGen) in 2025. National Airspace System (NAS) delays for the 2025 demand projected by the Transportation Systems Analysis Models (TSAM) were assessed using NASA s Airspace Concept Evaluation System (ACES). The shift in demand from commercial airline to automobile and from one airline route to another was investigated by adding the route delays determined from the ACES simulation to the travel times used in the TSAM and re-generating new flight scenarios. The ACES simulation results from this study determined that NextGen Operational Improvements alone do not provide sufficient airport capacity to meet the projected demand for passenger air travel in 2025 without significant system delays. Using larger aircraft with more seats on high-demand routes and introducing new direct routes, where demand warrants, significantly reduces delays, complementing NextGen improvements. Another significant finding of this study is that the adaptive behavior of passengers to avoid congested airline-routes is an important factor when projecting demand for transportation systems. Passengers will choose an alternative mode of transportation or alternative airline routes to avoid congested routes, thereby reducing delays to acceptable levels for the 2025 scenario; the penalty being that alternative routes and the option to drive increases overall trip time by 0.4% and may be less convenient than the first-choice route.

  10. Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments.

    PubMed

    Vaishampayan, Parag; Moissl-Eichinger, Christine; Pukall, Rüdiger; Schumann, Peter; Spröer, Cathrin; Augustus, Angela; Roberts, Anne Hayden; Namba, Greg; Cisneros, Jessica; Salmassi, Tina; Venkateswaran, Kasthuri

    2013-07-01

    Two strains of aerobic, non-motile, Gram-reaction-positive cocci were independently isolated from geographically distinct spacecraft assembly clean room facilities (Kennedy Space Center, Florida, USA and Centre Spatial Guyanais, Kourou, French Guiana). A polyphasic study was carried out to delineate the taxonomic identity of these two isolates (1P05MA(T) and KO_PS43). The 16S rRNA gene sequences exhibited a high similarity when compared to each other (100 %) and lower than 96.7 % relatedness with Arthrobacter crystallopoietes ATCC 15481(T), Arthrobacter luteolus ATCC BAA-272(T), Arthrobacter tumbae DSM 16406(T) and Arthrobacter subterraneus DSM 17585(T). In contrast with previously described Arthrobacter species, the novel isolates maintained their coccidal morphology throughout their growth and did not exhibit the rod-coccus life cycle typically observed in nearly all Arthrobacter species, except A. agilis. The distinct taxonomic identity of the novel isolates was confirmed based on their unique cell-wall peptidoglycan type (A.11.20; Lys-Ser-Ala2) and polar lipid profile (presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and two unknown glycolipids). The G+C content of the genomic DNA was 70.6 mol%. The novel strains revealed MK-9(H2) and MK-8(H2) as dominant menaquinones and exhibited fatty acid profiles consisting of major amounts of anteiso-C15 : 0 and anteiso-C17 : 0 and moderate amounts of iso-C15 : 0 discriminating them again from closely related Arthrobacter species. Based on these observations, the authors propose that strains 1P05MA(T) and KO_PS43 be assigned into a separate genus Tersicoccus gen. nov. For this new taxon, comprising strains 1P05MA(T) and KO_PS43, we propose the name Tersicoccus phoenicis gen. nov., sp. nov. (the type species of Tersicoccus), represented by the type strain Tersicoccus phoenicis 1P05MA(T) ( = NRRL B-59547(T) = DSM 30849(T)). PMID:23223813

  11. GenSo-EWS: a novel neural-fuzzy based early warning system for predicting bank failures.

    PubMed

    Tung, W L; Quek, C; Cheng, P

    2004-05-01

    Bank failure prediction is an important issue for the regulators of the banking industries. The collapse and failure of a bank could trigger an adverse financial repercussion and generate negative impacts such as a massive bail out cost for the failing bank and loss of confidence from the investors and depositors. Very often, bank failures are due to financial distress. Hence, it is desirable to have an early warning system (EWS) that identifies potential bank failure or high-risk banks through the traits of financial distress. Various traditional statistical models have been employed to study bank failures [J Finance 1 (1975) 21; J Banking Finance 1 (1977) 249; J Banking Finance 10 (1986) 511; J Banking Finance 19 (1995) 1073]. However, these models do not have the capability to identify the characteristics of financial distress and thus function as black boxes. This paper proposes the use of a new neural fuzzy system [Foundations of neuro-fuzzy systems, 1997], namely the Generic Self-organising Fuzzy Neural Network (GenSoFNN) [IEEE Trans Neural Networks 13 (2002c) 1075] based on the compositional rule of inference (CRI) [Commun ACM 37 (1975) 77], as an alternative to predict banking failure. The CRI based GenSoFNN neural fuzzy network, henceforth denoted as GenSoFNN-CRI(S), functions as an EWS and is able to identify the inherent traits of financial distress based on financial covariates (features) derived from publicly available financial statements. The interaction between the selected features is captured in the form of highly intuitive IF-THEN fuzzy rules. Such easily comprehensible rules provide insights into the possible characteristics of financial distress and form the knowledge base for a highly desired EWS that aids bank regulation. The performance of the GenSoFNN-CRI(S) network is subsequently benchmarked against that of the Cox's proportional hazards model [J Banking Finance 10 (1986) 511; J Banking Finance 19 (1995) 1073], the multi-layered perceptron (MLP) and the modified cerebellar model articulation controller (MCMAC) [IEEE Trans Syst Man Cybern: Part B 30 (2000) 491] in predicting bank failures based on a population of 3635 US banks observed over a 21 years period. Three sets of experiments are performed-bank failure classification based on the last available financial record and prediction using financial records one and two years prior to the last available financial statements. The performance of the GenSoFNN-CRI(S) network as a bank failure classification and EWS is encouraging. PMID:15109685

  12. The experimenter's museum: GenBank, natural history, and the moral economies of biomedicine.

    PubMed

    Strasser, Bruno J

    2011-03-01

    Today, the production of knowledge in the experimental life sciences relies crucially on the use of biological data collections, such as DNA sequence databases. These collections, in both their creation and their current use, are embedded in the experimentalist tradition. At the same time, however, they exemplify the natural historical tradition, based on collecting and comparing natural facts. This essay focuses on the issues attending the establishment in 1982 of GenBank, the largest and most frequently accessed collection of experimental knowledge in the world. The debates leading to its creation-about the collection and distribution of data, the attribution of credit and authorship, and the proprietary nature of knowledge-illuminate the different moral economies at work in the life sciences in the late twentieth century. They offer perspective on the recent rise of public access publishing and data sharing in science. More broadly, this essay challenges the big picture according to which the rise of experimentalism led to the decline of natural history in the twentieth century. It argues that both traditions have been articulated into a new way of producing knowledge that has become a key practice in science at the beginning of the twenty-first century. PMID:21667776

  13. Aureitalea marina gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from seawater.

    PubMed

    Park, Sanghwa; Yoshizawa, Susumu; Inomata, Kentaro; Kogure, Kazuhiro; Yokota, Akira

    2012-04-01

    An irregular rod-shaped, non-gliding, yellow-pigmented bacterium was isolated from seawater from the western North Pacific Ocean near Japan. The strain, designated S1-66T, was Gram-negative, obligately aerobic, heterotrophic and oxidase-positive. Growth occurred in the presence of 1-4?% NaCl, with optimum growth at 2?% NaCl. The strain grew at 15-30 °C, with optimum growth at 20-25 °C. The G+C content of genomic DNA was 48.1 mol% (HPLC). The predominant isoprenoid quinone was MK-6 and the major cellular fatty acids were iso-C15:0 (26.4?%), iso-C15:1 (20.3?%) and iso-C17:0 3-OH (14.2?%). Phylogenetic trees generated by using 16S rRNA gene sequences revealed that strain S1-66T belongs to the family Flavobacteriaceae and showed 94.2?% sequence similarity to the most closely related type strain, Ulvibacter antarcticus IMCC3101T. On the basis of phenotypic and phylogenetic features, S1-66T is classified in a novel genus and species within the family Flavobacteriaceae, for which the name Aureitalea marina gen. nov., sp. nov. is proposed. The type strain of Aureitalea marina is S1-66T (=NBRC 107741T=KCTC 23434T). PMID:21669922

  14. Aureicoccus marinus gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from seawater.

    PubMed

    Park, Sanghwa; Yoshizawa, Susumu; Muramatsu, Yuki; Nakagawa, Yasuyoshi; Yokota, Akira; Kogure, Kazuhiro

    2013-05-01

    A coccoid and amorphous-shaped, non-gliding, proteorhodopsin-containing, yellow bacterium, designated strain SG-18(T), was isolated from seawater in the western North Pacific Ocean near Japan. The strain was Gram-stain-negative, obligately aerobic, heterotrophic and oxidase-positive. It hydrolysed aesculin but not DNA, urea, gelatin or agar. Growth occurred in the presence of 1-5?% NaCl, with optimum growth at 2?% NaCl. The strain grew at 15-37 °C with an optimum temperature of 25-30 °C. The DNA G+C content of the genomic DNA of strain SG-18(T) was 47.0 mol% (HPLC). The predominant isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C15?:?1 G, iso-C15?:?0, iso-C15?:?0 3-OH. Phylogenetic trees generated by using 16S rRNA gene sequences revealed that strain SG-18(T) belonged to the family Flavobacteriaceae and showed 92.7?% sequence similarity to the most closely related species, Croceitalea eckloniae DOKDO 025(T). On the basis of phenotypic and phylogenetic features, strain SG-18(T) is classified as representing a novel species of a new genus within the family Flavobacteriaceae, for which the name Aureicoccus marinus gen. nov., sp. nov. is proposed. The type strain of the type species is SG-18(T) (?=?NBRC 108814(T)?=?KCTC 23967(T)). PMID:23002047

  15. Perexilibacter aurantiacus gen. nov., sp. nov., a novel member of the family 'Flammeovirgaceae' isolated from sediment.

    PubMed

    Yoon, Jaewoo; Ishikawa, Shu; Kasai, Hiroaki; Yokota, Akira

    2007-05-01

    A strictly aerobic, Gram-negative, gliding, dull-orange-pigmented, rod-shaped bacterium, designated strain Shu-F-UV2-2(T), was isolated from sediment (Carp Island, Republic of Palau) and was the focus of a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated to the family 'Flammeovirgaceae' of the phylum Bacteroidetes and that it showed highest sequence similarity (85.5 %) to Flammeovirga yaeyamensis NBRC 100898(T). The novel isolate could be differentiated phenotypically and physiologically from recognized members of the family 'Flammeovirgaceae'. The G+C content of the DNA was 43.0 mol%, MK-7 was the major menaquinone and iso-C(15 : 0), C(16 : 1)omega7c and C(16 : 1)omega5c were the major fatty acids. On the basis of this polyphasic evidence, it was concluded that strain Shu-F-UV2-2(T) represents a novel species in a new genus of the family 'Flammeovirgaceae', for which the name Perexilibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain is Shu-F-UV2-2(T) (=MBIC06993(T)=IAM 15413(T)=KCTC 12867(T)). PMID:17473242

  16. Ilumatobacter fluminis gen. nov., sp. nov., a novel actinobacterium isolated from the sediment of an estuary.

    PubMed

    Matsumoto, Atsuko; Kasai, Hiroki; Matsuo, Yoshihide; Omura, Satoshi; Shizuri, Yoshikazu; Takahashi, Y?ko

    2009-06-01

    Bacterial strain YM22-133T was isolated from the sediment of an estuary and grew in media with an artificial seawater base. Strain YM22-133T was Gram-positive, aerobic, non-motile and rod shaped. The cell-wall peptidoglycan contained LL-DAP, glycine, alanine and hydroxyglutamate. The predominant menaquinone was MK-9 (H8), with MK-9 (H0), MK-9 (H2), MK-9 (H4) and MK-9 (H6) present as minor menaquinones. The G+C content of the genomic DNA from the strain was 68 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is nearest to Acidimicrobium ferrooxidans DSM 10331T. However, the similarity is relatively low (87.1%) and the physiological characteristics are also different: Acidimicrobium ferrooxidans is thermotolerant and acidophilic. Therefore, strain YM22-133T can be classified as a novel genus and species, Ilumatobacter fluminis gen. nov., sp. nov. (type strain YM22-133T = DSM 18936T = MBIC 08263T). PMID:19590147

  17. Tepidicella xavieri gen. nov., sp. nov., a betaproteobacterium isolated from a hot spring runoff.

    PubMed

    França, Luis; Rainey, Fred A; Nobre, M Fernanda; da Costa, Milton S

    2006-04-01

    Strains TU-16T and TU-18, two non-pigmented bacterial isolates with an optimum growth temperature of about 45 degrees C and an optimum pH of about 8.5-9.0, were recovered from the Furnas geothermal area on the Island of São Miguel in the Azores. Phylogenetic analysis of the 16S rRNA gene sequence of these strains indicated that they represent a novel species in a new genus of the phylum Betaproteobacteria. The major fatty acids of strains TU-16T and TU-18 were 16 : 0 and 18 : 1omega7c. Ubiquinone 8 was the major respiratory quinone and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The novel isolates were aerobic; thiosulfate was oxidized to sulfate in the presence of a metabolizable carbon source. The organism assimilated organic acids and amino acids, but did not assimilate carbohydrates or polyols. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that strain TU-16T (=LMG 23030T = CIP 108724T) represents the type strain of a novel species in a new genus, Tepidicella xavieri gen. nov., sp. nov. PMID:16585714

  18. Mobilitalea sibirica gen. nov., sp. nov., a halotolerant polysaccharide-degrading bacterium.

    PubMed

    Podosokorskaya, O A; Bonch-Osmolovskaya, E A; Beskorovaynyy, A V; Toshchakov, S V; Kolganova, T V; Kublanov, I V

    2014-08-01

    A novel strictly anaerobic, halotolerant, organotrophic bacterium, strain P3M-3(T), was isolated from a microbial mat formed under the flow of hot water emerging from a 2775 m-deep well in Tomsk region (western Siberia, Russia). Cells of strain P3M-3(T) were straight and curved rods, 0.2-0.4 µm in width and 1.5-20 µm in length. Strain P3M-3(T) grew optimally at 37 °C, pH 7.0-7.5 and in a NaCl concentration of 15 g l(-1). Under optimum growth conditions, the doubling time was 1 h. The isolate was able to ferment a variety of mono-, di- and polysaccharides, including microcrystalline cellulose. Acetate, ethanol, H2 and CO2 were the main products of glucose fermentation. The DNA G+C content was 33.4 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain P3M-3(T) was a member of family Lachnospiraceae, whose representatives are also found in Clostridium cluster XIVa. 16S rRNA gene sequence similarity with Clostridium jejuense HY-35-12(T), the closest relative, was 93.9%. A novel genus and species, Mobilitalea sibirica gen. nov., sp. nov., are proposed based on phylogenetic analysis and physiological properties of the novel isolate. The type strain of the type species is P3M-3(T) (?=?DSM 26468(T)?=?VKM B-2804(T)). PMID:24827706

  19. Synthetic and Enhanced Vision Systems for NextGen (SEVS) Simulation and Flight Test Performance Evaluation

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Kramer, Lynda J.; Ellis,Kyle K.; Rehfeld, Sherri A.

    2012-01-01

    The Synthetic and Enhanced Vision Systems for NextGen (SEVS) simulation and flight tests are jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA). The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SEVS operational and system-level performance capabilities. Nine test flights (38 flight hours) were conducted over the summer and fall of 2011. The evaluations were flown in Gulfstream.s G450 flight test aircraft outfitted with the SEVS technology under very low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 ft to 2400 ft visibility) into various airports from Louisiana to Maine. In-situ flight performance and subjective workload and acceptability data were collected in collaboration with ground simulation studies at LaRC.s Research Flight Deck simulator.

  20. Guggenheimella bovis gen. nov., sp. nov., isolated from lesions of bovine dermatitis digitalis.

    PubMed

    Wyss, C; Dewhirst, F E; Paster, B J; Thurnheer, T; Luginbühl, A

    2005-03-01

    Dermatitis digitalis is an economically important ulcerative disease of undetermined aetiology affecting the hooves of cattle. Material was examined from two independent cases of this disease in Switzerland. Cultures from the advancing front of both lesions yielded large numbers of closely related short, mesophilic, non-motile, non-spore-forming, anaerobic, proteolytic, Gram-positive rods. The 16S rRNA gene sequences of strains OMZ 913(T) and OMZ 915 were identical and indicate Tindallia magadiensis and Eubacterium saphenum as their closest relatives. Phenotypically, the novel isolates are clearly distinguished from related bacteria by protein and antigen patterns, by cellular fatty acids and by API ZYM activities. The diamino acid of the Gram-positive cell wall is ornithine and the G+C content of OMZ 913(T) DNA is 44.4 mol%. The phylogenetic distance from recognized taxa in the phylum Firmicutes is sufficient to place these bovine isolates into a novel genus and species, for which the name Guggenheimella bovis gen. nov., sp. nov. is proposed, with OMZ 913(T) (=CIP 108087(T)=DSM 15657(T)) as the type strain. PMID:15774641

  1. A new captorhinid reptile, Gansurhinus qingtoushanensis, gen. et sp. nov., from the Permian of China.

    PubMed

    Reisz, Robert R; Liu, Jun; Li, Jin-Ling; Müller, Johannes

    2011-05-01

    Captorhinids, a clade of Paleozoic reptiles, are represented by a rich fossil record that extends from the Late Carboniferous into the Late Permian. Representatives of this clade dispersed from the equatorial regions of Laurasia into the temperate regions of Pangea during the Middle and Late Permian. This rich fossil record shows that there was an evolutionary trend from faunivorous to omnivorous and herbivorous feeding habits within this clade. The discovery of well-preserved captorhinid materials in the Middle Permian of China allows us to determine that the new taxon, Gansurhinus qingtoushanensis, gen. et sp. nov, is a member of Moradisaurinae, a clade of captorhinids with multiple tooth rows arranged in parallel. The presence of this moradisaurine in the Middle Permian of south central Asia leads us to suggest that paleogeographic changes during the Permian, with part of what is today China becoming a large peninsula of Pangea, allowed these early reptiles as well as other terrestrial vertebrates to extend their geographic ranges to this region of the Late Paleozoic supercontinent. PMID:21484260

  2. Celoporthe dispersa gen. et sp. nov. from native Myrtales in South Africa

    PubMed Central

    Nakabonge, Grace; Gryzenhout, Marieka; Roux, Jolanda; Wingfield, Brenda D.; Wingfield, Michael J.

    2006-01-01

    In a survey for Cryphonectria and Chrysoporthe species on Myrtales in South Africa, a fungus resembling the stem canker pathogen Chrysoporthe austroafricana was collected from native Syzygium cordatum near Tzaneen (Limpopo Province), Heteropyxis canescens near Lydenburg (Mpumalanga Province) and exotic Tibouchina granulosa in Durban (KwaZulu-Natal Province). The fungus was associated with dying branches and stems on S. cordatum, H. canescens and T. granulosa. However, morphological differences were detected between the unknown fungus from these three hosts and known species of Chrysoporthe. The aim of this study was to characterise the fungus using DNA sequence comparisons and morphological features. Pathogenicity tests were also conducted to assess its virulence on Eucalyptus (ZG 14 clones), H. natalensis and T. granulosa. Plants of H. canescens were not available for inoculation. Results showed distinct morphological differences between the unknown fungus and Chrysoporthe spp. Phylogenetic analysis showed that isolates reside in a clade separate from Chrysoporthe and other related genera. Celoporthe dispersa gen. et sp. nov. is, therefore, described to accommodate this fungus. Pathogenicity tests showed that C. dispersa is not pathogenic to H. natalensis, but that it is a potential pathogen of Eucalyptus and Tibouchina spp. PMID:18490984

  3. GenSAA: A tool for advancing satellite monitoring with graphical expert systems

    NASA Technical Reports Server (NTRS)

    Hughes, Peter M.; Luczak, Edward C.

    1993-01-01

    During numerous contacts with a satellite each day, spacecraft analysts must closely monitor real time data for combinations of telemetry parameter values, trends, and other indications that may signify a problem or failure. As satellites become more complex and the number of data items increases, this task is becoming increasingly difficult for humans to perform at acceptable performance levels. At the NASA Goddard Space Flight Center, fault-isolation expert systems have been developed to support data monitoring and fault detection tasks in satellite control centers. Based on the lessons learned during these initial efforts in expert system automation, a new domain-specific expert system development tool named the Generic Spacecraft Analyst Assistant (GenSAA) is being developed to facilitate the rapid development and reuse of real-time expert systems to serve as fault-isolation assistants for spacecraft analysts. Although initially domain-specific in nature, this powerful tool will support the development of highly graphical expert systems for data monitoring purposes throughout the space and commercial industry.

  4. Diddensiella caesifluorescens gen. nov., sp. nov., a riboflavin-producing yeast species of the family Trichomonascaceae.

    PubMed

    Péter, Gábor; Dlauchy, Dénes; Price, Neil P J; Kurtzman, Cletus P

    2012-12-01

    Four strains of a novel heterothallic yeast species were isolated from rotten wood collected in or near the Pilis Mountains in Hungary. The strains produced riboflavin in liquid culture. Analysis of gene sequences for the D1/D2 domains of the LSU nuclear rRNA, as well as analysis of concatenated gene sequences for the D1/D2 nuclear LSU rRNA, mitochondrial SSU rRNA and cytochrome oxidase II placed the novel species in a small clade including only two recognized species, Candida santjacobensis and Candida transvaalensis, in the family Trichomonascaceae. DNA sequence analyses demonstrated that the novel species was distinct from all currently recognized teleomorphic yeast genera. The name Diddensiella caesifluorescens gen nov., sp. nov. is proposed to accommodate the novel genus and species. The new genus proposed here can be recognized only from gene sequence analysis, because the characters of its asexual reproduction and ascospore formation are shared by several members of the genera Trichomonascus, Sugiyamaella and Spencermartinsiella. The type and isotype strains of D. caesifluorescens are NCAIM Y.01949(T) (?= NRRL Y-48781(T) = CBS 12613(T)) and NCAIM Y.01956(I) (?= NRRL Y-48782(I)?=?CBS 12614(I)), respectively. In view of their close relatedness to D. caesifluorescens, C. santjacobensis and C. transvaalensis are transferred to the genus Diddensiella as new combinations in accordance with changes in the International Code of Nomenclature for algae, fungi and plants. PMID:22843712

  5. Lombardia GENS: a collaborative registry for monogenic diseases associated with stroke

    PubMed Central

    Bersano, Anna; Baron, Pierluigi; Lanfranconi, Silvia; Trobia, Nadia; Sterzi, Roberto; Motto, Cristina; Comi, Giancarlo; Sessa, Maria; Martinelli-Boneschi, Filippo; Micieli, Giuseppe; Ferrarese, Carlo; Santoro, Patrizia; Parati, Eugenio; Boncoraglio, Giorgio; Padovani, Alessandro; Pezzini, Alessandro; Candelise, Livia

    2012-01-01

    Summary The Italian region of Lombardy, with its existing stroke centers and high-technology laboratories, provides a favorable context for studying monogenic diseases associated with stroke. The Lombardia GENS project was set up to create a regional network for the diagnosis of six monogenic diseases associated with stroke: CADASIL, Fabry disease, MELAS, familial and sporadic hemiplegic migraine, hereditary cerebral amyloid angiopathy and Marfan syndrome. The network comprises 36 stroke centers and seven high-technology laboratories, performing molecular analysis. In this context, all stroke/TIA patients fulfilling clinical criteria for monogenic diseases are currently being included in an ongoing study. Demographic, clinical and family data and diagnostic criteria are collected using standardized forms. On the basis of stroke incidence in Lombardy and the reported prevalence of the diseases considered, we expect, during the course of the study, to collect datasets and DNA samples from more than 200 stroke patients suspected of having monogenic diseases. This will allow evaluation of the regional burden and better phenotype characterization of monogenic diseases associated with stroke. PMID:23158583

  6. Longimycelium tulufanense gen. nov., sp. nov., a filamentous actinomycete of the family Pseudonocardiaceae.

    PubMed

    Xia, Zhan-Feng; Guan, Tong-Wei; Ruan, Ji-Sheng; Huang, Ying; Zhang, Li-Li

    2013-08-01

    A novel filamentous actinomycete strain, designated TRM 46004(T), was isolated from sediment of Aiding Lake in Tulufan Basin (42° 64' N 89° 26' E), north-west China. The isolate was characterized using a polyphasic approach. The isolate formed abundant aerial mycelium with few branches and vegetative mycelium, occasionally twisted and coiled; spherical sporangia containing one to several spherical spores developed at the ends of short sporangiophores on aerial mycelium. The G+C content of the DNA was 65.2 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and xylose, galactose and ribose as the major whole-cell sugars. The diagnostic phospholipids were phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H10). The major fatty acids were iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TRM 46004(T) formed a distinct lineage within the family Pseudonocardiaceae and showed 91.7-96.1 % 16S rRNA gene sequence similarity with members of the family Pseudonocardiaceae. On the basis of the evidence from this polyphasic study, a novel genus and species, Longimycelium tulufanense gen. nov., sp. nov., are proposed. The type strain of Longimycelium tulufanense is TRM 46004(T) (= CGMCC 4.5737(T) = NBRC 107726(T)). PMID:23315412

  7. Parasutterella excrementihominis gen. nov., sp. nov., a member of the family Alcaligenaceae isolated from human faeces.

    PubMed

    Nagai, Fumiko; Morotomi, Masami; Sakon, Hiroshi; Tanaka, Ryuichiro

    2009-07-01

    A novel, strictly anaerobic, non-spore-forming, Gram-negative coccobacillus (strain YIT 11859(T)) was isolated from human faeces. Biochemically, this strain was largely unreactive and was asaccharolytic. Growth of strain YIT 11859(T) in peptone-yeast extract broth produced no visible turbidity, and a trace amount of propionate was detected as an end product of metabolism. 16S rRNA gene sequence analysis showed that strain YIT 11859(T) was related most closely to the type strains of Sutterella species, with 90.8-88.0 % sequence similarity. Phylogenetic analysis of these and other related sequences confirmed that strain YIT 11859(T) was phylogenetically most closely associated with Sutterella species, but formed a separate cluster, indicating that strain YIT 11859(T) represents a novel member of the family Alcaligenaceae. Fatty acid analysis demonstrated the presence of a high concentration of C(18 : 1)omega9c (75 % of the total). The main respiratory quinones were menaquinone (MK-6) and methylated menaquinone (MMK-6). The G+C content of the DNA was 49.8 mol%. These results suggest that strain YIT 11859(T) represents a novel species of a new genus, for which the name Parasutterella excrementihominis gen. nov., sp. nov. is proposed. The type strain of Parasutterella excrementihominis is YIT 11859(T) (=DSM 21040(T) =JCM 15078(T)). PMID:19542131

  8. Psychrosphaera saromensis gen. nov., sp. nov., within the family Pseudoalteromonadaceae, isolated from Lake Saroma, Japan.

    PubMed

    Park, Sanghwa; Yoshizawa, Susumu; Hamasaki, Koji; Kogure, Kazuhiro; Yokota, Akira

    2010-01-01

    Three Gram-negative, motile, coccoid- and ellipsoidal-shaped, non-pigmented, chemoheterotrophic bacteria, designated strains SA4-31, SA4-46 and SA4-48(T), were isolated from Lake Saroma in Japan and subjected to a polyphasic taxonomical study. 16S rRNA gene sequence analysis revealed that the novel isolates could be affiliated to the family Pseudoalteromonadaceae of the order Alteromonadales. The strains shared approximately 99.7-100% sequence similarity with each other and showed 89.5-93.2% similarity with members of the family Pseudoalteromonadaceae with validly published names. The DNA-DNA relatedness among the strains SA 4-31, SA 4-46 and SA 4-48(T) was higher than 80%, a value that is accepted as a phylogenetic definition of one species. The DNA G+C contents of the three strains were 38.7-39.6 mol%. The major isoprenoid quinone was Q-8 and C16:0, C16:1 ?7c, C18:1 ?7c and C12:1 3OH were the major fatty acids. Based on the evidence from the polyphasic taxonomical study, it was concluded that the three strains should be classified as representing a new genus and species of the family Pseudoalteromonadaceae, for which the name Psychrosphaera saromensis gen. nov., sp. nov. (type strain SA4-48(T) =NBRC 107123(T)= KCTC 23240(T)) is proposed. PMID:21282903

  9. Development of Complexity Science and Technology Tools for NextGen Airspace Research and Applications

    NASA Technical Reports Server (NTRS)

    Holmes, Bruce J.; Sawhill, Bruce K.; Herriot, James; Seehart, Ken; Zellweger, Dres; Shay, Rick

    2012-01-01

    The objective of this research by NextGen AeroSciences, LLC is twofold: 1) to deliver an initial "toolbox" of algorithms, agent-based structures, and method descriptions for introducing trajectory agency as a methodology for simulating and analyzing airspace states, including bulk properties of large numbers of heterogeneous 4D aircraft trajectories in a test airspace -- while maintaining or increasing system safety; and 2) to use these tools in a test airspace to identify possible phase transition structure to predict when an airspace will approach the limits of its capacity. These 4D trajectories continuously replan their paths in the presence of noise and uncertainty while optimizing performance measures and performing conflict detection and resolution. In this approach, trajectories are represented as extended objects endowed with pseudopotential, maintaining time and fuel-efficient paths by bending just enough to accommodate separation while remaining inside of performance envelopes. This trajectory-centric approach differs from previous aircraft-centric distributed approaches to deconfliction. The results of this project are the following: 1) we delivered a toolbox of algorithms, agent-based structures and method descriptions as pseudocode; and 2) we corroborated the existence of phase transition structure in simulation with the addition of "early warning" detected prior to "full" airspace. This research suggests that airspace "fullness" can be anticipated and remedied before the airspace becomes unsafe.

  10. Pararotylenchus n. gen. (Pararotylenchinae n. subfam., Hoplolaimidae) with Six New Species and Two New Combinations

    PubMed Central

    Baldwin, J. G.; Bell, A. H.

    1981-01-01

    A new subfamily, Pararotylenchinae, (Hoplolaimidae) is described. It includes a single genus, Pararotylenchus n. gen., six new species, attd two new combinations, Pararotylenchus (syn. Tylenchorhynchus) brevicaudatus (Hopper, 1959) n. comb. and Pararotylenchus (syn. Rotylenchus) pint (Mamiya, 1968) n. comb. Pararotylenchinae is similar to certain other Hoplolaimidae, such as Rotylenchinae, with respect to most characters including the short tail, the position of the phasmids near the anus, and the relatively great distance of the dorsal gland orifice from the base of the stylet knobs. The lip region, as observed with the scanning electron microscope, conforms to the basic pattern for Hoplolaimidae. The labial disc is round with slit-like amphidial openings at the lateral sides of the periphery of the disc. The distinctive anterior-most lip annule is segmented into six sectors. Unlike other Hoplolaimidae, however, the esophageal glands of Pararotylenchinae form a basal bulb similar to that of Tylenchorhynchidae; other characters do not resemble Tylencborhynchidae. Specimens of Pararotylenchus have been recovered only from cool regions at high elevations and Pacific coastal areas in the Western United States, Japan, and Korea. PMID:19300732

  11. Four New Species of Heteroderidae Including Ekphymatodera n. gen. from California.

    PubMed

    Baldwin, J G; Bernard, E C; Mundo-Ocampo, M

    1989-01-01

    Four new species and a new genus of Heteroderidae from California are described, and their significance for phylogenetic analysis of the family is discussed. The new genus with type species, Ekphymatodera thomasoni n. gen., n. sp., shares many characteristics with Hylonema Luc, Taylor, &Cadet, 1978, but it is distinguished by its much greater vulva-anus distance and unique cuticular pattern. Hypotheses of relationships of Ekphymatodera and Hylonema with Sarisodera Wouts and Sher, 1971 versus Heterodera Schmidt, 1871 are discussed. Verutus californicus n. sp. is larger than the type species, Verutus volvingentis Esser, 1981, differing in females particularly by the greater distance of its excretory pore from the anterior end. Monophyly of Verutus, which may be an outgroup of all other Heteroderidae, is strengthened by description of V. californicus. Atalodera trilineata n. sp. differs from other ataloderines by having second-stage juveniles with three lateral lines and from the type, Atalodera ucri Wouts and Sher, 1971, by the more subtle cuticular pattern of females and longer juveniles with much longer tails. Atalodera festucae n. sp., with four lateral lines in juveniles, has smaller females than A. trilineata and has a protruding dorsal vulval lip. A unique common ancestor for Atalodera-Sherodera-Thecavermiculatus is supported, and monophyly with Thecavermieulatus andinus Golden, Franco, Jatala, &Astocaza, 1973 is considered. PMID:19287576

  12. Katatopygia gen. n., a monophyletic branch segregated from Boletina (Diptera, Mycetophilidae)

    PubMed Central

    Martinsson, Svante; Kjærandsen, Jostein

    2012-01-01

    Abstract The genus Katatopygia gen. n. is proposed for the Boletina erythropyga/punctus-group that was first introduced by Garrett (1924, 1925) and currently comprises eight described species. Molecular studies have strongly indicated that this group forms a monophyletic sister-group to a clade consisting of all other Boletina, Coelosia and Gnoriste, and its monophyly is supported by morphological data as well. The new genus includes the following species: Katatopygia antoma (Garrett, 1924), comb. n., Katatopygia antica (Garrett, 1924), comb. n., Katatopygia erythropyga (Holmgren, 1883), comb. n.,Katatopygia hissarica (Zaitzev & Polevoi, 2002), comb. n., Katatopygia magna (Garrett, 1925), comb. n., Katatopygia laticauda (Saigusa, 1968), comb. n., Katatopygia neoerythropyga (Zaitzev & Polevoi, 2002), comb. n. andKatatopygia sahlbergi (Lundström, 1906), comb. n., all transferred from Boletina. Katatopygia sahlbergi is found to be a senior synonym of Boletina punctus Garrett, 1925, syn. n. A phylogeny based on morphological data and using parsimony analysis yielded four most parsimonious trees where the new genus is retrieved as monophyletic with high support. Katatopygia neoerythropyga is found to be the sister-taxon to all other species that form two clades, one with Katatopygia sahlbergi-like species and one with Katatopygia erythropyga-like species. A key to males of Katatopygia is provided. PMID:22451790

  13. GenInfoGuard--a robust and distortion-free watermarking technique for genetic data.

    PubMed

    Iftikhar, Saman; Khan, Sharifullah; Anwar, Zahid; Kamran, Muhammad

    2015-01-01

    Genetic data, in digital format, is used in different biological phenomena such as DNA translation, mRNA transcription and protein synthesis. The accuracy of these biological phenomena depend on genetic codes and all subsequent processes. To computerize the biological procedures, different domain experts are provided with the authorized access of the genetic codes; as a consequence, the ownership protection of such data is inevitable. For this purpose, watermarks serve as the proof of ownership of data. While protecting data, embedded hidden messages (watermarks) influence the genetic data; therefore, the accurate execution of the relevant processes and the overall result becomes questionable. Most of the DNA based watermarking techniques modify the genetic data and are therefore vulnerable to information loss. Distortion-free techniques make sure that no modifications occur during watermarking; however, they are fragile to malicious attacks and therefore cannot be used for ownership protection (particularly, in presence of a threat model). Therefore, there is a need for a technique that must be robust and should also prevent unwanted modifications. In this spirit, a watermarking technique with aforementioned characteristics has been proposed in this paper. The proposed technique makes sure that: (i) the ownership rights are protected by means of a robust watermark; and (ii) the integrity of genetic data is preserved. The proposed technique-GenInfoGuard-ensures its robustness through the "watermark encoding" in permuted values, and exhibits high decoding accuracy against various malicious attacks. PMID:25689741

  14. Haplomyxa saranae gen. nov. et sp. nov., a new naked freshwater foraminifer.

    PubMed

    Dellinger, Marc; Labat, Amandine; Perrouault, Loïc; Grellier, Philippe

    2014-05-01

    A new naked foraminifer, Haplomyxa saranae gen. nov. sp. nov., is described from an established cell line made from a single cell isolated from a freshwater garden pond. The new species was morphologically close to Reticulomyxa filosa, the only valid naked freshwater foraminifer species. However the two species differed when it came to the morphology of the cell body, the number of cysts, and the nutrition. The 18S rRNA gene had one of the longest sequences to date (4863 nucleotides), and it contained many insertions that are typical of Foraminifera. The size of this gene was 45% longer than the one of R. filosa due to the elongation of A+T rich regions, but molecular phylogeny based on conserved regions of the 3'-end placed the new species in the same morphological clade K. This report includes both morphological and genetic data which undoubtedly show that the new species is a new naked freshwater foraminifer and the second species of the clade K. PMID:24810177

  15. Humibacter albus gen. nov., sp. nov., isolated from sewage sludge compost.

    PubMed

    Vaz-Moreira, Ivone; Nobre, M Fernanda; Ferreira, António C Silva; Schumann, Peter; Nunes, Olga C; Manaia, Célia M

    2008-04-01

    A bacterial strain isolated from sewage sludge compost, strain SC-083T, was characterized. The isolate was a motile, Gram-positive, short rod, forming coryneform V-shaped cells during the early stages of growth. The organism was strictly aerobic and able to grow between 22 and 36 degrees C and between pH 5.5 and 8.0. The predominant fatty acids were cyclohexyl-C17 : 0, anteiso-C17 : 0 and iso-C16 : 0, the major respiratory quinones were menaquinone 11 (MK-11) and 12 (MK-12), and the genomic DNA G+C content was 68 mol%. The peptidoglycan contained the diagnostic diamino acids ornithine and 2,4-diaminobutyric acid and was of acetyl type. The 16S rRNA gene sequence analysis indicated that this isolate belongs to the family Microbacteriaceae with the type strains of the species Leifsonia xyli (96 % gene sequence similarity), Leifsonia shinshuensis (96 %), Leifsonia naganoensis (95 %), Leifsonia aquatica (95 %), Agromyces ramosus (95 %) and Curtobacterium citreum (95 %) among the closest phylogenetic neighbours. The phylogenetic analysis and phenetic characteristics support the proposal of a new genus and a novel species, with the name Humibacter albus gen. nov., sp. nov. The type strain of Humibacter albus is SC-083T (=DSM 18994T =CCUG 54538T =LMG 23996T). PMID:18398211

  16. Kabataia gen. n., a new genus proposed for Microsporidium spp. infecting trunk muscles of fishes.

    PubMed

    Lom, J; Dyková, I; Tonguthai, K

    1999-10-11

    Based on a fine structural study, a new genus, Kabataia gen. n., is proposed for Microsporidium arthuri Lom, Dyková and Shaharom, 1990. It develops in trunk muscles of a South-East Asian freshwater fish, Pangasius sutchi. The genus has nuclei isolated throughout the cycle, merogony stages are multinucleate, sporogony proceeds in 2 steps: multinucleate sporont segments into sporoblast mother cells which produce 2 sporoblasts. Sporoblasts and early spores are characterized by a dense globule at the site of the posterior vacuole. Mature spores are of a rather variable shape. Their exospore is raised into small, irregular fields. The polaroplast is relatively small and its posterior part consists of flat vesicles with dense contents. The polar tube makes a small number (4 to 6) of turns. A congeneric species is Kabataia seriolae (Egusa, 1982) comb. nov. from cultured marine yellowtails Seriola quinqueradiata. Kabataia inflicts heavy damage on muscle tissue. The sarcoplasm within which Kabataia develops is reduced to an amorphous mass with tubule-like fibrils, microfibrils and small vesicles. PMID:10590927

  17. A new tardigrade, Mutaparadoxipus duodigifinis gen. nov., sp. nov. (Heterotardigrada: Arthrotardigrada), from the Southeastern United States.

    PubMed

    Gross, Vladimir; Miller, William R; Hochberg, Rick

    2014-01-01

    A new genus and species of Arthrotardigrada is described from Florida, USA based on its unique adhesive pad/claw combinations. Mutaparadoxipus duodigifinis gen. nov., sp. nov., is characterized by well-developed, ventral secondary clavae that are adjacent to the mouth, pointed lateral and caudal alae, seminal receptacles with coiled ducts opening lateral to the gonopore, and all legs with digits bearing proximal adhesive pads. Distal claws are present on digits I-III of legs I-III, but are missing from digit IV. On leg IV, distal claws are present only on digits II & III. A single accessory point is present on claws II & III only. This is the fourth species discovered to date with proximal adhesive pads, increasing support for a clade of adhesive-padded arthrotardigrades, and is likely the sister taxon of Paradoxipus orzeliscoides. The incomplete set of claws may represent an evolutionary step in a progressive loss of claws hypothesized to have occurred within the Halechiniscidae. The subfamily Orzeliscinae is amended as a result. PMID:25081448

  18. Sediminicoccus rosea gen. nov. sp. nov., isolated from the sediment of a eutrophic lake.

    PubMed

    Qu, Jian-Hang; Qu, Jian-Ying; He, Xiao-Bing; Li, Hai-Feng; Luo, Yu; Yin, Yan-Li; Zhai, Huan-Chen; Cai, Jing-Ping

    2013-01-01

    A polyphasic study was carried out to clarify the taxonomic position of a novel strain R-30(T) isolated from the surficial layer of sediment from Taihu Lake of China. The strain formed pink colored colonies comprising coccodial cells on R2A agar. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain R-30(T) clustered with the strains of genus Roseococcus and strain Rubritepida flocculans, with Roseococcus suduntuyensis SHET(T) as the closest relative, sharing 95.6% similarity. The major fatty acids (?5%) were 18?1?7c (66.7%), 16? 1?7c/16?1?6c (10.2%) and 16?0 (8.0%). The major polar lipids were diphosphatidyl glycerol (DPG), phosphatidyl methylethanolamine (PME), phosphatidyl ethanolamine (PE) and phosphatidyl choline (PC). The genomic DNA G+C content was 73.9 mol%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics, we conclude that strain R-30(T) represents a novel genus and species of the family Acetobacteraceae, for which we propose the name Sediminicoccus rosea gen nov. sp. nov. with R-30(T) (= CGMCC 1.12302(T) = NBRC 109675(T)) as the type species and type strain. PMID:24492604

  19. Using Game Theoretic Models to Predict Pilot Behavior in NextGen Merging and Landing Scenario

    NASA Technical Reports Server (NTRS)

    Yildiz, Yildiray; Lee, Ritchie; Brat, Guillaume

    2012-01-01

    In this paper, we present an implementation of the Semi Network-Form Game framework to predict pilot behavior in a merging and landing scenario. In this scenario, two aircraft are approaching to a freeze horizon with approximately equal distance when they become aware of each other via an ADS-B communication link that will be available in NextGen airspace. Both pilots want to gain advantage over the other by entering the freeze horizon earlier and obtain the first place in landing. They re-adjust their speed accordingly. However, they cannot simply increase their speed to the maximum allowable values since they are concerned with safety, separation distance, effort, possibility of being vectored-off from landing and possibility of violating speed constraints. We present how to model these concerns and the rest of the system using semi network-from game framework. Using this framework, based on certain assumptions on pilot utility functions and on system configuration, we provide estimates of pilot behavior and overall system evolution in time. We also discuss the possible employment of this modeling tool for airspace design optimization. To support this discussion, we provide a case where we investigate the effect of increasing the merging point speed limit on the commanded speed distribution and on the percentage of vectored aircraft.

  20. Heterorhabditidoides chongmingensis gen. nov., sp. nov. (Rhabditida: Rhabditidae), a novel member of the entomopathogenic nematodes.

    PubMed

    Zhang, Chongxing; Liu, Jingrui; Xu, Mingxu; Sun, Jie; Yang, Shouyun; An, Xianhui; Gao, Guofu; Lin, Maosong; Lai, Ren; He, Ziyi; Wu, Yidong; Zhang, Keyun

    2008-06-01

    During a recent soil sample survey in Eastern China, a new entomopathogenic nematode species, collected from the Chongming Islands in the southern-eastern area of Shanghai, was discovered. Morphological characteristics of different developmental stages of the nematode combined with molecular data showed that this nematode is a new genus of Rhabditidae, and described as Heterorhabditidoides chongmingensis gen. nov., sp. nov., for that it shares more morphological characteristics with heterorhabditids than with steinernematids. For males, the papillae formula of bursa is 1, 2, 3, 3, with constant papillae number in the terminal group, stoma tubular-shaped and about 1.5 head width; cheilorhabdions cuticularized, esophageal collar present and long, median bulb present. For infective juveniles, EP=90 (80-105)microm, ES=104 (92-120)microm, tail length=111 (89-159)microm, and a=19.1 (15-21). The percentages of the nucleotides A, T, C and G in the ITS1 regions of the new species are significantly different from those of heterorhabditids and other rhabditids. Molecular phylogenetic trees based on 18S rDNA and the internal transcribed spacer (ITS) sequences data revealed that the new entomopathogenic nematode species forms a monophyletic group, which is a sister group of the clade comprised of some genera of Rhabditidae. PMID:18410943

  1. Control Control Control: A Reassessment and Comparison of GenBank and Chromatogram mtDNA Sequence Variation in Baltic Grey Seals (Halichoerus grypus)

    PubMed Central

    Fietz, Katharina; Graves, Jeff A.; Olsen, Morten Tange

    2013-01-01

    Genetic data can provide a powerful tool for those interested in the biology, management and conservation of wildlife, but also lead to erroneous conclusions if appropriate controls are not taken at all steps of the analytical process. This particularly applies to data deposited in public repositories such as GenBank, whose utility relies heavily on the assumption of high data quality. Here we report on an in-depth reassessment and comparison of GenBank and chromatogram mtDNA sequence data generated in a previous study of Baltic grey seals. By re-editing the original chromatogram data we found that approximately 40% of the grey seal mtDNA haplotype sequences posted in GenBank contained errors. The re-analysis of the edited chromatogram data yielded overall similar results and conclusions as the original study. However, a significantly different outcome was observed when using the uncorrected dataset based on the GenBank haplotypes. We therefore suggest disregarding the existing GenBank data and instead using the correct haplotypes reported here. Our study serves as an illustrative example reiterating the importance of quality control through every step of a research project, from data generation to interpretation and submission to an online repository. Errors conducted in any step may lead to biased results and conclusions, and could impact management decisions. PMID:23977362

  2. Dactylogyrids (Platyhelminthes: Monogenoidea) parasitizing butterfly fishes (Teleostei: Chaetodontidae) from the coral reefs of Palau, Moorea, Wallis, New Caledonia, and Australia: species of Euryhaliotrematoides n. gen. and Aliatrema n. gen.

    PubMed

    Plaisance, Laetitia; Kritsky, Delane C

    2004-04-01

    Seven species of Euryhaliotrematoides n. gen. and 1 species of Aliatrema n. gen. (Monogenoidea; Dactylogyridae) are described and reported from the gills of 15 species of butterfly fishes (Chaetodontidae) from the coral reefs of Moorea (French Polynesia), Wallis (Wallis and Futuna), Heron and Lizard (Australia), Palau (Micronesia), and New Caledonia: Aliatrema cribbi n. sp. from Chaetodon auriga, Chaetodon lunula, Chaetodon trifasciatus, Chaetodon ulietensis, Chaetodon vagabundus, Forcipiger flavisissimus, and Heniochus chrysostomus; Euryhaliotrematoides annulocirrus n. comb. from C. auriga, C. lunula, and C. vagabundus; Euryhaliotrematoides aspistis n. sp. from C. auriga, Chaetodon citrinellus, C. lunula, Chaetodon reticulatus, C. ulietensis, and C. vagabundus; Euryhaliotrematoides berenguelae n. sp. from C. citrinellus, Chaetodon ornatissimus, and F. flavisissimus; Euryhaliotrematoides grandis n. comb. from C. auriga, C. citrinellus, Chaetodon ephippium, Chaetodon kleinii, Chaetodon lineolatus, C. lunula, C. ornatissimus, C. trifasciatus, C. vagabundus, and H. chrysostomus; Euryhaliotrematoides microphallus n. comb. from C. auriga, C. citrinellus, C. ephippium, C. kleinii, C. lunula, C. ornatissimus, C. reticulatus, Chaetodon trifascialis, C. trifasciatus, C. vagabundus, F. flavisissimus, and H. chrysostomus; Euryhaliotrematoides pirulum n. sp. from C. auriga, C. citrinellus, C. lunula, C. trifasciatus, and C. vagabundus; and Euryhaliotrematoides triangulovagina n. comb. from C. auriga, C. citrinellus, C. kleinii, C. lunula, C. ornatissimus, C. vagabundus, F. flavisissimus, H. chrysostomus, and Hemitaurichthys polylepis. All reports of previously described species are new locality records. With exceptions of E. grandis and E. annulocirrus on C. auriga and C. lunula and E. triangulovagina and E. microphallus on C. auriga, all reports are new host records. Haliotrema hainanensis and H. affinis are considered junior subjective synonyms of E. triangulovagina and E. annulocirrus, respectively. Aliatrema n. gen. is characterized by marine dactylogyrids with tandem gonads (germarium pretesticular), haptoral hooks with upright acute thumbs, a coiled copulatory organ with counterclockwise rings and funnel-shaped base but lacking an accessory piece, and a dextral vaginal pore. Euryhaliotrematoides n. gen. is characterized by marine dactylogyrids having tandem gonads (germarium pretesticular), haptoral hooks with upright acute thumbs, a coiled copulatory organ with counterclockwise rings and funnel-shaped base, a vas deferens looping the left intestinal cecum, and a dextral vaginal pore. PMID:15165056

  3. Exploring Gen Y Responses to an Apparel Brand’s Use of Cause-Related Marketing Does Message Matter When It Comes to Support for the Breast Cancer Cause?

    Microsoft Academic Search

    Karen H. Hyllegard; Jennifer Paff Ogle; Ruoh-Nan Yan; Julianne Attmann

    2010-01-01

    This study explored Gen Y’s responses to cause-related marketing (CRM) in apparel advertising. Data were collected from 349 Gen Y consumers to examine the influence of CRM on attitudes and purchase intentions toward an apparel brand. Attitude toward the brand was predicted by awareness of the apparel brand, perception of CRM, evaluation of the advertisement, involvement in the breast cancer

  4. Visual advantage of enhanced flight vision system during NextGen flight test evaluation

    NASA Astrophysics Data System (ADS)

    Kramer, Lynda J.; Harrison, Stephanie J.; Bailey, Randall E.; Shelton, Kevin J.; Ellis, Kyle K. E.

    2014-06-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment. Simulation and flight tests were jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA) to evaluate potential safety and operational benefits of SVS/EFVS technologies in low visibility Next Generation Air Transportation System (NextGen) operations. The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SVS/EFVS operational and system-level performance capabilities. Nine test flights were flown in Gulfstream's G450 flight test aircraft outfitted with the SVS/EFVS technologies under low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 feet to 3600 feet reported visibility) under different obscurants (mist, fog, drizzle fog, frozen fog) and sky cover (broken, overcast). Flight test videos were evaluated at three different altitudes (decision altitude, 100 feet radar altitude, and touchdown) to determine the visual advantage afforded to the pilot using the EFVS/Forward-Looking InfraRed (FLIR) imagery compared to natural vision. Results indicate the EFVS provided a visual advantage of two to three times over that of the out-the-window (OTW) view. The EFVS allowed pilots to view the runway environment, specifically runway lights, before they would be able to OTW with natural vision.

  5. Paenalcaligenes hominis gen. nov., sp. nov., a new member of the family Alcaligenaceae.

    PubMed

    Kämpfer, P; Falsen, E; Langer, S; Lodders, N; Busse, H-J

    2010-07-01

    A beige-pigmented bacterium (strain CCUG 53761A(T)) was isolated from human blood from an 85-year-old man in Göteborg, Sweden. Comparative analysis of 16S rRNA gene sequences showed that this bacterium displayed <95 % similarity to all described species of the genera of the family Alcaligenaceae. It grouped within the radiation of the genus Alcaligenes, but showed only 93.0-94.8 % similarity to type strains of members of this genus (Alcaligenes faecalis subsp. parafaecalis, 94.8 %; Alcaligenes faecalis subsp. faecalis, 94.2 %; Alcaligenes faecalis subsp. phenolicus, 93.4 %). This discrimination was supported by chemotaxonomic differences. The polyamine pattern consisted of the predominant compound putrescine, moderate amounts of spermidine and minor to trace amounts of spermine and cadaverine; 2-hydroxyputrescine was not detectable. The quinone system was ubiquinone Q-8 with minor amounts of Q-7. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylethanolamine and moderate amounts of phosphatidylglycerol and an unknown phospholipid; minor lipids were also detected. The fatty acid profile, with large amounts of C(16 : 0) and C(17 : 0) cyclo and the absence of C(12 : 0) 2-OH as hydroxylated fatty acid, also differed significantly from those reported for Alcaligenes species. On the basis of these data, it is proposed that strain CCUG 53761A(T) represents a novel genus and species, for which the name Paenalcaligenes hominis gen. nov., sp. nov. is proposed. The type strain of Paenalcaligenes hominis is CCUG 53761A(T) =CCM 7698(T). PMID:19684310

  6. Thermotunica guangxiensis gen. nov., sp. nov., isolated from mushroom residue compost.

    PubMed

    Wu, Hao; Lian, Yunpeng; Liu, Bin; Ren, Yanling; Qin, Peisheng; Huang, Fuchang

    2014-05-01

    A novel thermophilic actinomycete, designated AG2-7T, was isolated from mushroom residue compost in Guangxi University, Nanning, China. The strain grew optimally at 45-60 °C, at pH 7.0 and with 0-3.0% (w/v) NaCl. Vegetative mycelia were branched and whitish to pale yellow without fragmentation. Aerial mycelium was abundant, whitish and differentiated into long chains of spores, with a membranous structure or tunica partially covering the surface of aerial hyphae. The non-motile spores were oval in shape with a ridged surface. Strain AG-27T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were galactose and ribose. Major fatty acids were iso-C16:0 (27.51%), iso-C17:0 (10.47%) and anteiso-C17:0 (12.01%). MK-9(H4) was the predominant menaquinone. The polar phospholipids were diphosphatidylglycerol, ninhydrin-positive glycophospholipid, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylethanolamine, phosphatidylmethylethanolamine, an unknown phospholipid and unknown glucosamine-containing phospholipids. The G+C content of the genomic DNA was 63.6 mol%. 16S rRNA gene sequence analysis showed that the organism belonged to the family Pseudonocardiaceae, suborder Pseudonocardineae and showed more than 5% divergence from other members of the family. Based on the phenotypic and phylogenetic data, strain AG2-7T represents a novel species of a new genus in the family Pseudonocardiaceae, for which the name Thermotunica guangxiensis gen. nov., sp. nov. is proposed. The type strain of the type species is AG2-7T (=ATCC BAA-2499T=CGMCC 4.7099T). PMID:24488931

  7. Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity.

    PubMed

    Sizova, Maria V; Muller, Paul; Panikov, Nicolai; Mandalakis, Manolis; Hohmann, Tine; Hazen, Amanda; Fowle, William; Prozorov, Tanya; Bazylinski, Dennis A; Epstein, Slava S

    2013-04-01

    A strictly anaerobic Gram-stain-variable but positive by structure, non-spore-forming bacterium designated Lachnospiraceae bacterium ACC2 strain DSM 24645(T) was isolated from human subgingival dental plaque. Bacterial cells were 4-40 µm long non-motile rods, often swollen and forming curved filaments up to 200 µm. Cells contained intracellular, poorly crystalline, nanometre-sized iron- and sulfur-rich particles. The micro-organism was able to grow on yeast extract, trypticase peptone, milk, some sugars and organic acids. The major metabolic end-products of glucose fermentation were butyrate, lactate, isovalerate and acetate. The growth temperature and pH ranges were 30-42 °C and 4.9-7.5, respectively. Major fatty acids were C14?:?0, C14?:?0 DMA (dimethyl aldehyde), C16?:?0, C16?:?1?7c DMA. The whole-cell hydrolysate contained meso-diaminopimelic acid, indicating peptidoglycan type A1?. The DNA G+C content was calculated to be 55.05 mol% from the whole-genome sequence and 55.3 mol% as determined by HPLC. There were no predicted genes responsible for biosynthesis of respiratory lipoquinones, mycolic acids and lipopolysaccharides. Genes associated with synthesis of teichoic and lipoteichoic acids, diaminopimelic acid, polar lipids and polyamines were present. According to the 16S rRNA gene sequence phylogeny, strain DSM 24645(T) formed, together with several uncultured oral clones, a separate branch within the family Lachnospiraceae, with the highest sequence similarity to the type strain of Moryella indoligenes at 94.2?%. Based on distinct phenotypic and genotypic characteristics, we suggest that strain DSM 24645(T) represents a novel species in a new genus, for which the name Stomatobaculum longum gen. nov., sp. nov. is proposed. The type strain of Stomatobaculum longum is DSM 24645(T) (?=?HM-480(T); deposited in BEI Resources, an NIH collection managed by the ATCC). PMID:22843721

  8. Halotia gen. nov., a phylogenetically and physiologically coherent cyanobacterial genus isolated from marine coastal environments.

    PubMed

    Genuário, Diego Bonaldo; Vaz, Marcelo Gomes Marçal Vieira; Hentschke, Guilherme Scotta; Sant'Anna, Célia Leite; Fiore, Marli Fátima

    2015-02-01

    Nostoc is a common and well-studied genus of cyanobacteria and, according to molecular phylogeny, is a polyphyletic group. Therefore, revisions of this genus are urged in an attempt to clarify its taxonomy. Novel strains isolated from underexplored environments and assigned morphologically to the genus Nostoc are not genetically related to the 'true Nostoc' group. In this study, four strains isolated from biofilms collected in Antarctica and five strains originated from Brazilian mangroves were evaluated. Despite their morphological similarities to other morphotypes of Nostoc, these nine strains differed from other morphotypes in ecological, physiological and genetic aspects. Based on the phylogeny of the 16S rRNA gene, the Antarctic sequences were grouped together with the sequences of the Brazilian mangrove isolates and Nostoc sp. Mollenhauer 1 : 1-067 in a well-supported cluster (74 % bootstrap value, maximum-likelihood). This novel cluster was separated phylogenetically from the 'true Nostoc' clade and from the clades of the morphologically similar genera Mojavia and Desmonostoc. The 16S rRNA gene sequences generated in this study exhibited 96 % similarity to sequences from the nostocacean genera mentioned above. Physiologically, these nine strains showed the capacity to grow in a salinity range of 1-10 % NaCl, indicating their tolerance of saline conditions. These results provide support for the description of a new genus, named Halotia gen. nov., which is related morphologically to the genera Nostoc, Mojavia and Desmonostoc. Within this new genus, three novel species were recognized and described based on morphology and internal transcribed spacer secondary structures: Halotia branconii sp. nov., Halotia longispora sp. nov. and Halotia wernerae sp. nov., under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants. PMID:25424485

  9. Halopenitus persicus gen. nov., sp. nov., an archaeon from an inland salt lake.

    PubMed

    Amoozegar, Mohammad Ali; Makhdoumi-Kakhki, Ali; Shahzadeh Fazeli, Seyed Abolhassan; Azarbaijani, Reza; Ventosa, Antonio

    2012-08-01

    A novel pale pink-pigmented halophilic archaeon, strain DC30(T), was isolated from Aran-Bidgol salt lake, a hypersaline playa in Iran. Cells of strain DC30(T) were non-motile and pleomorphic, from rods to triangular or disc-shaped. Strain DC30(T) required at least 1.7 M NaCl and 0.05 M MgCl(2) for growth (optimum, 3 M NaCl and 0.1 M MgCl(2)). The optimum pH and temperature for growth of strain DC30(T) were pH 7.5 and 40 °C, respectively, although it was capable of growth over pH and temperature ranges of 6.5-8.5 and 25-50 °C, respectively. Analysis of the 16S rRNA gene sequence showed that strain DC30(T) was a member of the family Halobacteriaceae. However, it had low 16S rRNA gene sequence similarities of 92.4%, 89.4% and 89.1% to the most closely related haloarchaeal taxa, the type species of the genera Halorubrum, Halogranum and Haloplanus, respectively. The DNA G+C content was 66.0 mol%. Phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, common phospholipids found in haloarchaea, were present. Three minor phospholipids and one unidentified glycolipid were also observed. The only quinone present was MK-8(II-H(2)). The physiological, biochemical and phylogenetic differences between strain DC30(T) and other previously described genera of extremely halophilic archaea suggest that strain DC30(T) represents a novel species in a new genus within the family Halobacteriaceae, for which the name Halopenitus persicus gen. nov., sp. nov. is proposed. The type strain of Halopenitus persicus is DC30(T) (?=?IBRC 10041(T)?=?KCTC 4046(T)). PMID:22003044

  10. Haloarchaeobius iranensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from a saline lake.

    PubMed

    Makhdoumi-Kakhki, A; Amoozegar, M A; Bagheri, M; Ramezani, M; Ventosa, A

    2012-05-01

    Strain EB21(T) was isolated from a brine sample from Aran-Bidgol salt lake, a saline playa in Iran. Strain EB21(T) was an orange-red-pigmented, motile rod and required at least 2 M NaCl but not MgCl(2) for growth. Optimal growth was achieved at 3.5 M NaCl and 0.2 M MgCl(2). The optimum pH and temperature for growth were pH 7.5 and 40 °C, while it was able to grow at pH 6.0-8.0 and 25-55 °C. Analysis of the 16S rRNA gene sequence revealed that strain EB21(T) is a member of the family Halobacteriaceae, showing low levels of similarity to other members of the family. The highest sequence similarities, 91.8, 91.7 and 91.5?%, were obtained with the 16S rRNA gene sequences of the type strains of Halobiforma lacisalsi, Haloterrigena thermotolerans and Halalkalicoccus tibetensis, respectively. Polar lipid analyses revealed that strain EB21(T) contains phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. Three unidentified glycolipids and one minor phospholipid were also observed. The only quinone present was MK-8(II-H(2)). The G+C content of its DNA was 67.7 mol%. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain EB21(T) is thus considered to represent a novel species in a new genus within the family Halobacteriaceae, order Halobacteriales, for which the name Haloarchaeobius iranensis gen. nov., sp. nov. is proposed. The type strain of Haloarchaeobius iranensis is EB21(T) (?=?IBRC-M 10013(T) ?=?KCTC 4048(T)). PMID:21685256

  11. Yuhushiella deserti gen. nov., sp. nov., a new member of the suborder Pseudonocardineae.

    PubMed

    Mao, Jun; Wang, Jian; Dai, Huan-Qin; Zhang, Zhi-Dong; Tang, Qi-Yong; Ren, Biao; Yang, Na; Goodfellow, Michael; Zhang, Li-Xin; Liu, Zhi-Heng

    2011-03-01

    A thermotolerant, Gram-stain-positive, aerobic, sporangium-forming actinomycete, strain RA45(T), was isolated from a desert region in Xinjiang Uigur Autonomous Region, north-western China. Comparative analysis of the 16S rRNA gene sequence and phenotypic characterization revealed that strain RA45(T) belonged phylogenetically to the family Pseudonocardiaceae of the suborder Pseudonocardineae. Strain RA45(T) showed more than 5? % 16S rRNA gene sequence divergence from recognized species of genera in the family Pseudonocardiaceae, forming a distinct lineage within the evolutionary radiation occupied by the genera Amycolatopsis, Prauserella, Thermocrispum, Saccharomonospora, Saccharopolyspora and Sciscionella, but distinct from each of them. The affiliation to the family was supported by the presence of suborder- and family-specific 16S rRNA signature nucleotides, a DNA G+C content of 69.9 mol%, the presence of meso-diaminopimelic acid, ribose, arabinose, glucose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes, the presence of menaquinone MK-9(H?) as the major respiratory lipoquinone, a lack of mycolic acids and the presence of an N-acetylated type of muramic acid. However, strain RA45(T) differed from known genera of the family in its polar lipid composition: the major phospholipids were phosphatidylethanolamine, phosphatidylinositol mannosides, phosphatidylmethylethanolamine, diphosphatidylglycerol, phospholipids of unknown structure and phospholipids of unknown structure containing glucosamine (phospholipid type IV). Based on its morphological, chemotaxonomic and phylogenetic characteristics, strain RA45(T) is considered to represent a novel species of a new genus in the family Pseudonocardiaceae, for which the name Yuhushiella deserti gen. nov., sp. nov. is proposed. The type strain of Yuhushiella deserti is RA45(T) (=CGMCC 4.5579(T) =JCM 16584(T)). PMID:20400669

  12. Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium.

    PubMed

    Tank, Marcus; Bryant, Donald A

    2015-05-01

    A novel anoxygenic photoheterotrophic member of the phylum Acidobacteria , Chloracidobacterium thermophilum strain B sp. nov., was isolated from a cyanobacterial enrichment culture derived from microbial mats associated with Octopus Spring, Yellowstone National Park, WY. C. thermophilum sp. nov. was a Gram-stain-negative rod (diameter, approximately 0.8-1.0 µm; variable length, approximately 2.5 µm), which formed greenish-brown liquid suspension cultures. It was a moderately thermophilic microaerophile and grew in a defined medium at 51 °C (Topt; range 44 to 58 °C) and in the pH range 5.5 to 9.5 (pHopt?=?~7.0). The DNA G+C content was 61.3 mol%, and phylogenetic analysis, based on the 16S rRNA sequence, showed that C. thermophilum sp. nov. belongs to subdivision 4 ( Acidobacteriaceae ) of the Acidobacteria . C. thermophilum sp. nov. was unable to synthesize branched-chain amino acids, l-lysine, and vitamin B12, which were required for growth. Although the organism lacked genes/enzymes for autotrophic carbon fixation, bicarbonate was required. Growth was stimulated by other amino acids and 2-oxoglutarate. Cells produced chlorosomes containing a diverse mixture of bacteriochlorophyll (BChl) c derivatives, and additionally, synthesized BChl a P, Chl a PD, and Zn-BChl a'P, which occurred in type-1 homodimeric reaction centres. The carotenoids included echinenone, canthaxanthin, lycopene, ?-carotene and ?-carotene. C. thermophilum sp. nov. produced iso-diabolic acid as its major fatty acid and synthesized three hopanoids (diploptene, bacteriohopanetetrol and bacteriohopanetetrol cyclitol ether). Based upon its phenotypic and genotypic properties, the name Chloracidobacterium thermophilum gen. nov., sp. nov. is proposed for this isolate; the type strain is C. thermophilum strain B(T) (ATCC BAA-2647?=?JCM 30199). PMID:25667398

  13. Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome

    PubMed Central

    Schmidt, Johanna; Taipale, Sami J.; Doolittle, W. Ford; Koll, Ulrike

    2014-01-01

    A pure culture of an actinobacterium previously described as ‘Candidatus Rhodoluna lacicola’ strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8T represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8T is noticeable due to its unusually low values of cell size (0.05 µm3), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8T is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8T and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3?%. The cell-wall peptidoglycan of strain MWH-Ta8T was of type B2? (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15?:?0 (36.5?%), iso-C16?:?0 (16.5?%), iso-C15?:?0 (15.6?%) and iso-C14?:?0 (8.9?%), and the major (>10?%) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8T represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8T (?=?DSM 23834T?=?LMG 26932T). PMID:24984700

  14. Gelria glutamica gen. nov., sp. nov., a thermophilic, obligately syntrophic, glutamate-degrading anaerobe.

    PubMed

    Plugge, Caroline M; Balk, Melike; Zoetendal, Erwin G; Stams, Alfons J M

    2002-03-01

    A novel anaerobic, gram-positive, thermophilic, spore-forming, obligately syntrophic, glutamate-degrading bacterium, strain TGO(T), was isolated from a propionate-oxidizing methanogenic enrichment culture. The axenic culture was obtained by growing the bacterium on pyruvate. Cells were rod-shaped and non-motile. The optimal temperature for growth was 50-55 degrees C and growth occurred between 37 and 60 degrees C. The pH range for growth was 5.5-8 with optimum growth at pH 7. In pure culture, strain TGO(T) could grow on pyruvate, lactate, glycerol and several sugars. In co-culture with the hydrogenotrophic methanogen Methanobacterium thermautotrophicum strain Z-245, strain TGO(T) could grow on glutamate, proline and Casamino acids. Glutamate was converted to H2, CO2, propionate and traces of succinate. Strain TGO(T) was not able to utilize sulphate, sulphite, thiosulphate, nitrate or fumarate as electron acceptors. The G+C content was 33.8 mol%. Sequence analysis of the 16S rDNA revealed that strain TGO(T) belongs to the thermophilic, endospore-forming anaerobes, though no close relations were found. Its closest relations were Moorella glycerini (92%) and Moorella thermoacetica (90%). Strain TGOT had an unusually long 16S rDNA of more than 1700 bp. The additional base pairs were found as long loops in the V1, V7 and V9 regions of the 16S rDNA. However, the loops were not found in the 16S rRNA. The name Gelria glutamica gen. nov., sp. nov. is proposed for strain TGO(T). PMID:11931148

  15. Brockia lithotrophica gen. nov., sp. nov., an anaerobic thermophilic bacterium from a terrestrial hot spring.

    PubMed

    Perevalova, Anna A; Kublanov, Ilya V; Baslerov, R V; Zhang, Gengxin; Bonch-Osmolovskaya, Elizaveta A

    2013-02-01

    A novel thermophilic bacterium, strain Kam1851(T), was isolated from a terrestrial hot spring of the Uzon Caldera, Kamchatka Peninsula, Russia. Cells of strain Kam1851(T) were spore-forming rods with a gram-positive type of cell wall. Growth was observed between 46 and 78 °C, and pH 5.5-8.5. The optimal growth (doubling time, 6.0 h) was at 60-65 °C and pH 6.5. The isolate was an obligate anaerobe growing in pre-reduced medium only. It grew on mineral medium with molecular hydrogen or formate as electron donors, and elemental sulfur, thiosulfate or polysulfide as electron acceptors. The main cellular fatty acids were C(16?:?0) (34.2?%), iso-C(16?:?0) (18?%), C(18?:?0) (12.8?%) and iso-C(17?:?0) (11.1?%). The G+C content of the genomic DNA of strain Kam1851(T) was 63 mol%. 16S rRNA gene sequence analysis showed that strain Kam1851(T) belonged to the order Thermoanaerobacterales, but it was not closely related to representatives of any genera with validly published names. The most closely related strains, which had no more than 89.2?% sequence similarity, were members of the genera Ammonifex and Caldanaerobacter. On the basis of its phylogenetic position and novel phenotypic features, isolate Kam1851(T) is proposed to represent a novel species in a new genus, Brockia lithotrophica gen. nov., sp. nov.; the type strain of Brockia lithotrophica is Kam1851(T) (?=?DSM 22653(T)?=?VKM B-2685(T)). PMID:22493174

  16. Salinispirillum marinum gen. nov., sp. nov., a haloalkaliphilic bacterium in the family 'Saccharospirillaceae'.

    PubMed

    Shahinpei, Azadeh; Amoozegar, Mohammad Ali; Fazeli, Seyed Abolhassan Shahzadeh; Schumann, Peter; Ventosa, Antonio

    2014-11-01

    A novel Gram-staining-negative, motile, non-pigmented, facultatively anaerobic, spirillum-shaped, halophilic and alkaliphilic bacterium, designated strain GCWy1(T), was isolated from water of the coastal-marine wetland Gomishan in Iran. The strain was able to grow at NaCl concentrations of 1-10% (w/v) and optimal growth was achieved at 3% (w/v). The optimum pH and temperature for growth were pH 8.5 and 30 °C, while the strain was able to grow at pH 7.5-10 and 4-40 °C. Phylogenetic analysis based on the comparison of the 16S rRNA gene sequence placed the isolate within the class Gammaproteobacteria as a separate deep branch, with 92.1% or lower sequence similarity to representatives of the genera Saccharospirillum and Reinekea and less than 91.0% sequence similarity with other remotely related genera. The major cellular fatty acids of the isolate were C(18 : 1)?7c, C(16:0) and C(17 : 0), and the major components of its polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cells of strain GCWy1(T) contained the isoprenoid quinones Q-9 and Q-8 (81% and 2%, respectively). The G+C content of the genomic DNA of this strain was 52.3 mol%. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain GCWy1(T) represents a novel species in a new genus in the family 'Saccharospirillaceae', order Oceanospirillales, for which the name Salinispirillum marinum gen. nov., sp. nov. is proposed. The type strain of the type species is GCWy1(T) (?= IBRC-M 10765(T)?=CECT 8342(T)). PMID:25062697

  17. Canaleparolina darwiniensis, gen. nov., sp. nov., and other pillotinaceous spirochetes from insects.

    PubMed

    Wier, A; Ashen, J; Margulis, L

    2000-12-01

    We describe two new pillotinaceous spirochetes (Canaleparolina darwiniensis, Diplocalyx cryptotermitidis) and identify for the first time Hollandina pterotermitidis from both the subterranean termite Cryptotermes cavifrons and the wood-eating cockroach Cryptocercus punctulatus based on morphometric analysis of transmission electron micrographic thin sections. C. darwiniensis, gen. nov., sp. nov., limited to near Darwin, Australia, invariably is present on the surface of the treponeme-studded trichomonad Mixotricha paradoxa, a consistent inhabitant of the hindgut of healthy termite Mastotermes darwiniensis. The spirochete both attached to the surface of protists and free-swimming in the paunch (hindgut) lumen of the insect has 16 periplasmic flagella (16:32:16) and imbricated wall structures that resemble flattened crenulations of Pillotina. The flagella surround half the protoplasmic cylinder. C. darwiniensis is the largest (0.5 microm diameter x 25 microm length) of the three epibiotic bacteria (two spirochetes, one rod) that comprise the complex cortex of its host Mixotricha paradoxa. Several criteria distinguish Diplocalyx cryptotermitidis sp. nov. isolated from Cryptotermes cavifrons intestine: smaller diameter, fewer flagella, absence of inner and outer coats of the outer membrane, wider angle subtended by its flagella and, most notably, cytoplasmic tubule-associated centers, which are periodic electron dense spheres within the protoplasmic cylinder from which emanate cytoplasmic tubules up to 24 nm in diameter. This is also the first report of abundant populations of Hollandina in Cryptotermes cavifrons (those populations belong to the species H. pterotermitidis). Morphometric analysis of the first thin sections of any spirochetes (published nearly 40 years ago by A.V. Grimstone) permits us to identify the large (0.9 microm diameter) free-swimming intestinal symbiont of Cryptocercus punctulatus also as Hollandina pterotermitidis. PMID:11334304

  18. Chryseomicrobium imtechense gen. nov., sp. nov., a new member of the family Planococcaceae.

    PubMed

    Arora, Pankaj Kumar; Chauhan, Archana; Pant, Bhawana; Korpole, Suresh; Mayilraj, Shanmugam; Jain, Rakesh Kumar

    2011-08-01

    A Gram-stain-positive, rod-shaped, yellow, non-motile, non-spore-forming, strictly aerobic bacterial strain, designated MW 10(T), was isolated from seawater of the Bay of Bengal, India, and was subjected to a polyphasic taxonomic study. Analysis of the 16S rRNA gene sequence revealed that strain MW 10(T) showed highest similarity to the type strains of Psychrobacillus psychrodurans (96.15 %) and Psychrobacillus psychrotolerans (96.01 %) and showed less than 96 % similarity to members of the genera Paenisporosarcina, Planococcus, Sporosarcina and Planomicrobium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MW 10(T) formed a clade separate from members of closely related genera. The morphological, physiological and chemotaxonomic characteristics of strain MW 10(T) differed from those of members of closely related genera. The major fatty acid in strain MW 10(T) was iso-C(15 : 0) and the menaquinones were MK-7 (48.4 %), MK-8 (32.3 %), MK-7(H(2)) (13.7 %) and MK-6 (5.6 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown phospholipid, an unknown lipid and an unknown glycolipid. The cell-wall peptidoglycan type was l-Lys-d-Asp. The genomic DNA G+C content (53.4 mol%) of strain MW 10(T) was significantly different from those of members of closely related genera. On the basis of its morphological, physiological and chemotaxonomic characteristics as well as our phylogenetic analysis, we conclude that strain MW 10(T) is a member of a novel genus and species, for which the name Chryseomicrobium imtechense gen. nov., sp. nov., is proposed. The type strain of Chryseomicrobium imtechense is MW 10(T) (?= MTCC 10098(T) ?= JCM 16573(T)). PMID:20833890

  19. High quality draft genome sequence and description of Occidentia massiliensis gen. nov., sp. nov., a new member of the family Rickettsiaceae

    PubMed Central

    2014-01-01

    The family Rickettsiaceae currently includes two genera: Orientia that contains one species, Orientiatsutsugamushi, and Rickettsia that contains 28 species. Occidentia massiliensis gen. nov., sp. nov. strain OS118T is the type strain of O. massiliensis gen. nov., sp. nov., the type species of the new genus Occidentia gen. nov. within the family Rickettsiaceae. This strain, whose genome is described here, was isolated in France from the soft tick Ornithodoros sonrai collected in Senegal. O. massiliensis is an aerobic, rod-shaped, Gram-negative, obligate intracellular bacillus that may be cultivated in BME/CTVM2 cells. Here we describe the features of O. massiliensis, together with the complete genomic sequencing and annotation. The 1,469,252 bp long genome (1 chromosome but no plasmid) contains 1,670 protein-coding and 41 RNA genes, including one rRNA operon. PMID:25780502

  20. Rhizonema sequoiae n.gen. n.sp. from Coast Redwood Sequoia sempervirens (D.Don) Endl.

    PubMed

    Del Prado Vera, I C; Lownsbery, B F; Maggenti, A R

    1983-07-01

    Rhizonema sequoiae n.gen, u. sp. is described from the roots of Coast Redwood, Sequoia sempervirens (D. Don) Endl., growing near Lake Lagunitas, Marin County, California. Rhizonema females are annulated over their entire bodies, are wholly embedded in host tissue, and secrete an abundant amount of gel material. Mature females do not form a cyst. The vulva is located on a large posterior terminal cone, and the anus is on the dorsal vulval lip. Esophageal glands of the second-stage larvae fill more than half of the body cavity. Tails of the vermiform males are blunt, and a cloacal tubus is present. PMID:19295834

  1. Australasian sequestrate fungi 18: Solioccasus polychromus gen. & sp. nov., a richly colored, tropical to subtropical, hypogeous fungus.

    PubMed

    Trappe, James M; Castellano, Michael A; Halling, Roy E; Osmundson, Todd W; Binder, Manfred; Fechner, Nigel; Malajczuk, Nicholas

    2013-01-01

    Solioccasus polychromus gen. & sp. nov., the most brightly colored hypogeous fungus known, is described from Papua New Guinea and tropical northern Australia south into subtropical forests along the Queensland coast and coastal mountains to near Brisbane. Phylogenetic analysis of molecular data places it as a sister genus to Bothia in the Boletineae, a clade of predominantly ectomycorrhizal boletes. Ectomycorrhizal trees, such as members of the Myrtaceae (Eucalyptus, Corymbia, Lophostemon, Melaleuca spp.) and Allocasuarina littoralis, were present usually in mixture or in some cases dominant, so we infer some or all of them to be among the ectomycorrhizal hosts of S. polychromus. PMID:23709482

  2. Comparison ofGen-Probe GroupA Streptococcus Direct Test withCulture forDiagnosing Streptococcal Pharyngitis

    Microsoft Academic Search

    EMILY A. VETTER; PETER C. WOLLAN; ANDFRANK R. COCKERILL

    1994-01-01

    TheGroupAStreptococcus Direct Test(GP-ST test; Gen-Probe, Inc., SanDiego, Calif.) wascompared with culture forthedetection ofStreptococcus pyogenes fromthroat swabsof767patients withpharyngitis. Swabs weretested bytheGP-STtest after inoculating a5%sheep bloodagar(SBA) plate. SBAplates wereincubated at35°Cinroomairfor72h.SBAplates withnoevidence ofbeta-hemolytic colonies after 18to24h of incubation weresubcultured bytaking aswipe across theprimary inoculum fromtheSBAplate toanagar selective forStreptococcus spp.Inalow-prevalence (11.9%) population andincomparison withthenumberof positive cultures detected bythe72-hsingle-culture method(SBAplate method), theGP-STtesthada sensitivity of88.6%, aspecificity

  3. Accuracy evaluation of ClimGen weather generator and daily to hourly disaggregation methods in tropical conditions

    NASA Astrophysics Data System (ADS)

    Safeeq, Mohammad; Fares, Ali

    2011-12-01

    Daily and sub-daily weather data are often required for hydrological and environmental modeling. Various weather generator programs have been used to generate synthetic climate data where observed climate data are limited. In this study, a weather data generator, ClimGen, was evaluated for generating information on daily precipitation, temperature, and wind speed at four tropical watersheds located in Hawai`i, USA. We also evaluated different daily to sub-daily weather data disaggregation methods for precipitation, air temperature, dew point temperature, and wind speed at M?kaha watershed. The hydrologic significance values of the different disaggregation methods were evaluated using Distributed Hydrology Soil Vegetation Model. MuDRain and diurnal method performed well over uniform distribution in disaggregating daily precipitation. However, the diurnal method is more consistent if accurate estimates of hourly precipitation intensities are desired. All of the air temperature disaggregation methods performed reasonably well, but goodness-of-fit statistics were slightly better for sine curve model with 2 h lag. Cosine model performed better than random model in disaggregating daily wind speed. The largest differences in annual water balance were related to wind speed followed by precipitation and dew point temperature. Simulated hourly streamflow, evapotranspiration, and groundwater recharge were less sensitive to the method of disaggregating daily air temperature. ClimGen performed well in generating the minimum and maximum temperature and wind speed. However, for precipitation, it clearly underestimated the number of extreme rainfall events with an intensity of >100 mm/day in all four locations. ClimGen was unable to replicate the distribution of observed precipitation at three locations (Honolulu, Kahului, and Hilo). ClimGen was able to reproduce the distributions of observed minimum temperature at Kahului and wind speed at Kahului and Hilo. Although the weather data generation and disaggregation methods were concentrated in a few Hawaiian watersheds, the results presented can be used to similar mountainous location settings, as well as any specific locations aimed at furthering the site-specific performance evaluation of these tested models.

  4. Modeling and Evaluating Pilot Performance in NextGen: Review of and Recommendations Regarding Pilot Modeling Efforts, Architectures, and Validation Studies

    NASA Technical Reports Server (NTRS)

    Wickens, Christopher; Sebok, Angelia; Keller, John; Peters, Steve; Small, Ronald; Hutchins, Shaun; Algarin, Liana; Gore, Brian Francis; Hooey, Becky Lee; Foyle, David C.

    2013-01-01

    NextGen operations are associated with a variety of changes to the national airspace system (NAS) including changes to the allocation of roles and responsibilities among operators and automation, the use of new technologies and automation, additional information presented on the flight deck, and the entire concept of operations (ConOps). In the transition to NextGen airspace, aviation and air operations designers need to consider the implications of design or system changes on human performance and the potential for error. To ensure continued safety of the NAS, it will be necessary for researchers to evaluate design concepts and potential NextGen scenarios well before implementation. One approach for such evaluations is through human performance modeling. Human performance models (HPMs) provide effective tools for predicting and evaluating operator performance in systems. HPMs offer significant advantages over empirical, human-in-the-loop testing in that (1) they allow detailed analyses of systems that have not yet been built, (2) they offer great flexibility for extensive data collection, (3) they do not require experimental participants, and thus can offer cost and time savings. HPMs differ in their ability to predict performance and safety with NextGen procedures, equipment and ConOps. Models also vary in terms of how they approach human performance (e.g., some focus on cognitive processing, others focus on discrete tasks performed by a human, while others consider perceptual processes), and in terms of their associated validation efforts. The objectives of this research effort were to support the Federal Aviation Administration (FAA) in identifying HPMs that are appropriate for predicting pilot performance in NextGen operations, to provide guidance on how to evaluate the quality of different models, and to identify gaps in pilot performance modeling research, that could guide future research opportunities. This research effort is intended to help the FAA evaluate pilot modeling efforts and select the appropriate tools for future modeling efforts to predict pilot performance in NextGen operations.

  5. Comparative Evaluation of Two PCR-Based Methods for Detection of Methicillin-Resistant Staphylococcus aureus (MRSA): Xpert MRSA Gen 3 and BD-Max MRSA XT.

    PubMed

    Lepainteur, Margaux; Delattre, Sandrine; Cozza, Sophie; Lawrence, Christine; Roux, Anne-Laure; Rottman, Martin

    2015-06-01

    We compared two walk-away molecular diagnostic assays, the GeneXpert MRSA Gen 3 assay and the BD-Max MRSA XT assay. A total of 119 prospective swabs and 36 culture-positive samples were tested. Xpert MRSA Gen 3 had sensitivity of 95.7% and specificity of 100% versus 87.5% and 97.1% for BD-Max. The difference in agreement with the enriched culture results was significantly in favor of the Xpert assay (P < 0.02, McNemar nonparametric text). PMID:25878336

  6. search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

    PubMed Central

    2013-01-01

    Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/. PMID:23452691

  7. A new genus and species of isanthid sea anemone (Cnidaria: Anthozoa: Actiniaria) from Chilean Patagonia, Anthoparactis fossii n. gen. et sp

    NASA Astrophysics Data System (ADS)

    Häussermann, Verena; Rodríguez, Estefanía

    2014-09-01

    We describe a new genus and species of sea anemone from Chilean Patagonia. Anthoparactis fossii n. gen. et sp. adds another acontiate genus and species to the family Isanthidae Carlgren, 1938. Anthoparactis n. gen. differs from the other isanthid genera in having the same number of mesenteries distally and proximally, acontia with basitrichs only, and a column with verrucae distally. Anthoparactis fossii n. sp. differs from the most similar species, Isoparactis fionae Lauretta et al., 2013, in the number of cycles of mesenteries and tentacles, structures of the column, colour pattern of the oral disc, cnidae, and geographical distribution. Isanthidae now includes seven genera and 11 species.

  8. Jeotgalibacillus alimentarius gen. nov., sp. nov., a novel bacterium isolated from jeotgal with L-lysine in the cell wall, and reclassification of Bacillus marinus Rüger 1983 . as mMrinibacillus marinus gen nov., comb. nov.

    PubMed

    Yoon, J H; Weiss, N; Lee, K C; Lee, I S; Kang, K H; Park, Y H

    2001-11-01

    A moderately halophilic, round-endospore-forming bacterium (strain YKJ-13T) was isolated from jeotgal, a traditional Korean fermented seafood, and studied by a polyphasic taxonomic approach. This organism was related to the phylogenetic clade comprising members of Bacillus rRNA group 2 and formed a cluster with Bacillus marinus with a bootstrap fidelity value of 93.6%. The peptidoglycan type was A1alpha linked directly through L-Lys. Based on cell morphology, peptidoglycan type and phylogeny, strain YKJ-13T, together with B. marinus, is considered to be a member of Bacillus rRNA group 2. Strain YKJ-13T was also characterized by having MK-7 and MK-8 as the predominant menaquinones and iso-C15:0 as the major fatty acid. The DNA G+C content was 44 mol%. Strain YKJ-13T exhibited a 16S rDNA similarity value of 95.7% with B. marinus DSM 1297T, its closest phylogenetic relative. Levels of 16S rDNA similarity between strain YKJ-13T and other Bacillus spp. were less than 94.2%. Therefore, on the basis of the data presented, the name Jeotgalibacillus alimentarius gen. nov., sp. nov. is proposed for strain YKJ-13T (= KCCM 80002T = JCM 10872T). It is also proposed that B. marinus be reclassified in Marinibacillus gen. nov. as Marinibacillus marinus comb. nov. PMID:11760951

  9. Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn's disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov.

    PubMed

    Würdemann, Dieco; Tindall, Brian J; Pukall, Rüdiger; Lünsdorf, Heinrich; Strömpl, Carsten; Namuth, Theresa; Nahrstedt, Hannes; Wos-Oxley, Melissa; Ott, Stephan; Schreiber, Stephan; Timmis, Kenneth N; Oxley, Andrew P A

    2009-06-01

    A strictly anaerobic, Gram-positive, short-rod/coccobacillus-shaped bacterial strain, designated 7-10-1-b(T), was isolated from the colon of a patient suffering from acute Crohn's disease. The isolate formed small, pale-white, semi-translucent colonies on solid cultivation media. The strain was catalase-positive and metabolized only a small number of carbon sources. Whole-cell fatty acids consisted predominantly of saturated fatty acids (89 %), of which 15 : 0 anteiso was the major component. The polar lipids phosphatidylglycerol and diphosphatidylglycerol as well as four glycolipids were identified. 16S rRNA gene sequence analysis revealed that the isolate represents a distinct lineage within the family Coriobacteriaceae and has 94.6 % identity to the type strain of [Eggerthella] hongkongensis, the phylogenetically closest bacterial species. On the basis of the analyses performed, the new genus and species Gordonibacter pamelaeae gen. nov., sp. nov. is described, with strain 7-10-1-b(T) (=DSM 19378(T) =CCUG 55131(T)) as the type and only strain of Gordonibacter pamelaeae. Also, based on the chemotaxonomic data obtained for all type strains of the neighbouring genus Eggerthella, we propose that Eggerthella hongkongensis Lau et al. 2006 be transferred to a new genus as Paraeggerthella hongkongensis gen. nov., comb. nov.; the type strain of Paraeggerthella hongkongensis is HKU10(T) (=DSM 16106(T) =CCUG 49250(T)). PMID:19502325

  10. Hemodynamic and Echocardiographic Profiles in African American Compared With White Offspring of Hypertensive Parents: The HyperGEN Study

    PubMed Central

    2014-01-01

    BACKGROUND Alterations in cardiovascular structure and function have been shown to precede the finding of elevated blood pressure. METHODS This study is part of the Hypertension Genetic Epidemiologic Network (HyperGEN) in which genetic and environmental determinants of hypertension were investigated in 5 geographical field centers. All nonhypertensive offspring (n = 1,035) were included from the entire HyperGEN study population that consists of 2,225 hypertensive patients and 1,380 nonhypertensive patients who had adequate echocardiographic left ventricular (LV) mass measurements. Participants were compared by self-declared race (African American and white). RESULTS Nonhypertensive African American offspring were younger (aged 31 years vs. 38 years), more likely to be female, and had a higher body mass index (BMI) and higher systolic blood pressure (SBP) than their white counterparts. After adjusting for age, sex, SBP, pulse pressure (PP), BMI, diabetes status, and family effects, we observed statistically significant and potentially pathophysiological differences (all with P ? 0.001) with greater LV mass/height, relative wall thickness, and posterior wall thickness and with lesser midwall shortening, PP/stroke volume, and (PP/stroke volume)/fat-free body mass. CONCLUSION This study shows that ethnic differences in hemodynamic and echocardiographic profiles exist in a large, population-based cohort of nonhypertensive offspring of hypertensive parents. PMID:24242823

  11. Chalicogloea cavernicola gen. nov., sp. nov. (Chroococcales, Cyanobacteria), from low-light aerophytic environments: combined molecular, phenotypic and ecological criteria.

    PubMed

    Roldán, M; Ramírez, M; del Campo, J; Hernández-Mariné, M; Komárek, J

    2013-06-01

    This work characterizes a unicellular cyanobacterium with nearly spherical cells and thin-outlined sheaths that divide irregularly, forming small packets immersed in a diffluent mucilaginous layer. It was isolated growing on calcite speleothems and walls in a show cave in Collbató (Barcelona, Spain). Spectral confocal laser and transmission electron microscopy were used to describe the morphology, fine structure and thylakoid arrangement. The pigments identified were phycoerythrin, phycocyanin, allophycocyanin and chlorophyll a. Three-dimensional reconstructions, generated from natural fluorescence z-stacks, revealed a large surface area of nearly flat, arm-like thylakoidal membranes connected to each other and forming a unified structure in a way that, to our knowledge, has never been described before. Phylogenetic analyses using the 16S rRNA gene sequence showed 95% similarity to strain Chroococcus sp. JJCM (GenBank accession no. AM710384). The diacritical phenotypic features do not correspond to any species currently described, and the genetic traits support the strain being classified as the first member of an independent genus in the order Chroococcales and the family Chroococcaceae. Hence, we propose the name Chalicogloea cavernicola gen. nov., sp. nov. under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants. The type strain of Chalicogloea cavernicola is COLL 3(T) (=CCALA 975(T) =CCAP 1424/1(T)). PMID:23178723

  12. Saliterribacillus persicus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a hypersaline lake.

    PubMed

    Amoozegar, Mohammad Ali; Bagheri, Maryam; Didari, Maryam; Shahzedeh Fazeli, Seyed Abolhassan; Schumann, Peter; Sánchez-Porro, Cristina; Ventosa, Antonio

    2013-01-01

    A novel Gram-positive, moderately halophilic bacterium, designated strain X4B(T), was isolated from soil around the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain X4B(T) were motile rods and formed ellipsoidal endospores at a terminal or subterminal position in swollen sporangia. Strain X4B(T) was a strictly aerobic bacterium, catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-22.5 % (w/v), with optimum growth occurring at 7.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. Analysis of 16S rRNA gene sequence revealed that strain X4B(T) is a member of the family Bacillaceae, constituting a novel phyletic lineage within this family. Highest sequence similarities were obtained with the 16S rRNA gene sequences of the type strains of Sediminibacillus albus (96.0 %), Paraliobacillus ryukyuensis (95.9 %), Paraliobacillus quinghaiensis (95.8 %) and Sediminibacillus halophilus (95.7 %), respectively. The DNA G+C content of this novel isolate was 35.2 mol%. The major cellular fatty acids of strain X4B(T) were anteiso-C(15 : 0) and anteiso-C(17 : 0) and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, two aminolipids, an aminophospholipid and an unknown phospholipid. The isoprenoid quinones were MK-7 (89 %) and MK-6 (11 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain X4B(T) represents a novel species in a new genus in the family Bacillaceae, order Bacillales for which the name Saliterribacillus persicus gen. nov., sp. nov. is proposed. The type strain of the type species (Saliterribacillus persicus) is X4B(T) ( = IBRC-M 10629(T) = KCTC 13827(T)). PMID:22447700

  13. The Australian Monstrilloida (Crustacea: Copepoda) I. Monstrillopsis Sars, Maemonstrilla Grygier & Ohtsuka, and Australomonstrillopsis gen. nov.

    PubMed

    Suárez-Morales, Eduardo; Mckinnon, A David

    2014-01-01

    Monstrilloid copepods were collected during zooplankton surveys in reef and coastal areas of Australia. Representatives of all four genera of the Monstrilloida (Monstrilla Dana, Monstrillopsis Sars, Cymbasoma Thompson, and Maemonstrilla Grygier & Ohtsuka) were recorded. In this contribution a taxonomic analysis of specimens belonging to the latter two genera is provided, and a new genus described. The genus Monstrillopsis was represented exclusively by male specimens, on the basis of which three new species are described: Mon. hastata sp. nov., Mon. boonwurrungorum sp. nov., and Mon. nanus sp. nov. These are distinguished from each other and previously described species of this genus by details of the genital complex (or genital apparatus), body size, ornamentation of the cephalic surface, number of caudal setae, and characteristic modifications of the fifth antennular segment. All have distinctive characters not associated with sexual modifications, which will ease the task of matching females collected in future studies. Australomonstrillopsis gen. nov. is proposed to accommodate a male specimen with a unique combination of characters including massively developed caudal rami, cephalic perioral protuberances, and absence of an inner seta on the first exopodal segment of legs 1-4, among other characters. The new genus is monotypic and contains A. crassicaudata sp. nov. Three of the four new species of Maemonstrilla (Mae. ohtsukai sp. nov., Mae. hoi sp. nov., and Mae. protuberans sp. nov.) belong to the Mae. hyottoko species group, and the remaining one, Mae. crenulata sp. nov., belongs to the Mae. turgida group. Each of the new species of Maemonstrilla from Australia can be distinguished from its known congeners by a unique combination of characters including the type of body reticulation, body size, antennule and body proportions, distinctive characters of the swimming legs, details of the antennular armature, and the presence/absence of a posteroventral process on the genital compound somite. With the addition of the four new species of Monstrillopsis and the four of Maemonstrilla described herein, the number of species in these genera has increased to 13 and 11 species, respectively. In no case did congeneric species co-occur, hinting that there may be a rich species diversity yet to be discovered within the Australian Monstrilloida. PMID:24871727

  14. The Photosynthetic Apparatus and Its Regulation in the Aerobic Gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov

    PubMed Central

    Spring, Stefan; Lünsdorf, Heinrich; Fuchs, Bernhard M.; Tindall, Brian J.

    2009-01-01

    Background There is accumulating evidence that in some marine environments aerobic bacteriochlorophyll a-producing bacteria represent a significant part of the microbial population. The interaction of photosynthesis and carbon metabolism in these interesting bacteria is still largely unknown and requires further investigation in order to estimate their contribution to the marine carbon cycle. Methodology/Principal Findings Here, we analyzed the structure, composition and regulation of the photosynthetic apparatus in the obligately aerobic marine gammaproteobacterium KT71T. Photoheterotrophically grown cells were characterized by a poorly developed lamellar intracytoplasmic membrane system, a type 1 light-harvesting antenna complex and a photosynthetic reaction center associated with a tetraheme cytochrome c. The only photosynthetic pigments produced were bacteriochlorophyll a and spirilloxanthin. Under semiaerobic conditions KT71T cells expressing a photosynthetic apparatus showed a light-dependent increase of growth yield in the range of 1.3–2.5 fold. The expression level of the photosynthetic apparatus depended largely on the utilized substrate, the intermediary carbon metabolism and oxygen tension. In addition, pigment synthesis was strongly influenced by light, with blue light exerting the most significant effect, implicating that proteins containing a BLUF domain may be involved in regulation of the photosynthetic apparatus. Several phenotypic traits in KT71T could be identified that correlated with the assumed redox state of growing cells and thus could be used to monitor the cellular redox state under various incubation conditions. Conclusions/Significance In a hypothetical model that explains the regulation of the photosynthetic apparatus in strain KT71T we propose that the expression of photosynthesis genes depends on the cellular redox state and is maximal under conditions that allow a balanced membrane redox state. So far, bacteria capable of an obligately aerobic, photosynthetic metabolism constitute a unique phenotype within the class Gammaproteobacteria, so that it is justified to propose a new genus and species, Congregibacter litoralis gen. nov, sp. nov., represented by the type strain KT71T (?=?DSM 17192T?=?NBRC 104960T). PMID:19287491

  15. Session A--Equipping Tomorrow's Fire Managers--Dicus USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 1

    E-print Network

    Standiford, Richard B.

    Session A--Equipping Tomorrow's Fire Managers--Dicus USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 1 Equipping Tomorrow's Fire Managers1 Christopher A. Dicus2 Abstract Fire managers's managers must be equipped with the skills necessary to understand and liaise with a burgeoning group

  16. Loose interpretation of the requirements. Where the plans had the requirements just like the existing house", the Builders used, in some cases, very loose interpretations of likeness. Gen-

    E-print Network

    Perry, Dewayne E.

    Loose interpretation of the requirements. Where the plans had the requirements just like the existing house", the Builders used, in some cases, very loose interpretations of likeness. Gen- erally that already exist in the house. In one sense, that requirement is in the design speci cation | at least

  17. Poster Session--Fuel Consumption During Prescribed Fires in Big Sage--Wright, Ottmar USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 363

    E-print Network

    Standiford, Richard B.

    Poster Session--Fuel Consumption During Prescribed Fires in Big Sage--Wright, Ottmar USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 363 Fuel Consumption During Prescribed Fires in Big Sage of operational prescribed fires in big sage (Artemisia tridentata) ecosystems throughout the interior West. Pre

  18. DIETS CONTAINING SOY PROTEIN ISOLATE (SPI) OR GENISTEIN (GEN) FED TO FEMALE RATS DURING PREGNANCY DO NOT SUPPRESS AZOXYMETHANE (AOM)-INDUCED INTESTINAL CANCERS IN THE MALE PROGENY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous studies showed that lifetime dietary SPI inhibits AOM-induced colon tumorigenesis when compared to casein (CAS)-containing control diet. The aim of this study was to investigate if cancer protection by dietary SPI or the soy isoflavone GEN is afforded in utero to progeny via dietary exposu...

  19. Session K--Postfire Mortality of Large Trees in Sierra Nevada--Fites-Kaufman, Weixelman, Merrill USDA Forest Service Gen. Tech. Rep. PSW-GTR-189 2008. 279

    E-print Network

    Standiford, Richard B.

    Session K--Postfire Mortality of Large Trees in Sierra Nevada--Fites-Kaufman, Weixelman, Merrill USDA Forest Service Gen. Tech. Rep. PSW-GTR-189 2008. 279 One-Year Postfire Mortality of Large Trees to 75 cm diameter at breast height (DBH), were tracked for post-fire mortality. The Star Fire, located

  20. INSTITUTE OF PHYSICS PUBLISHING JOURNAL OF PHYSICS A: MATHEMATICAL AND GENERAL J. Phys. A: Math. Gen. 36 (2003) 1079110805 PII: S0305-4470(03)61597-0

    E-print Network

    Ritort, Felix

    2003-01-01

    investigate violations of the fluctuation­dissipation theorem in two classes of trap models by studying and violations of the fluctuation­dissipation theorem (FDT) (for recent reviews see [6, 7]). FDT violations can. Gen. 36 (2003) 10791­10805 PII: S0305-4470(03)61597-0 Universal dependence of the fluctuation­dissipation

  1. Eriospermocormus indicus gen. et sp. nov. (Liliales: Eriospermaceae): first record of a monocotyledonous corm from the Deccan Intertrappean beds of India

    Microsoft Academic Search

    S. D. Bonde

    2005-01-01

    Eriospermocormus indicus gen. et sp. nov. is a permineralized monocotyledonous corm resembling Eriospermum Jacq. (Order Liliales, Family Eriospermaceae), described from the Deccan Intertrappean beds at Nawargaon, Wardha District, Maharashtra, India. It is a vertically and laterally compressed rhizomatous tuber exhibiting seven nodes within a height of 4.0cm. Fibrous roots emerge in rings from the internodes. The axis has a thin

  2. 57USDA Forest Service Gen. Tech. Rep. PSW-GTR-155. 1996. Data Management and Analysis of Ozone Injury to Pines Schilling and Duriscoe

    E-print Network

    Standiford, Richard B.

    included in the FOREST relational database. Plot Tree Whorl Index ID ID ID ID Forest Date Branch # EII Site57USDA Forest Service Gen. Tech. Rep. PSW-GTR-155. 1996. Data Management and Analysis of Ozone Forest Service's Pacific Southwest Research Station, Riverside, California. The field data were gathered

  3. Omemeea maxbassiensis n. gen., n. sp. (Nematoda: Aphelenchoididae) from Galleries of the Bark Beetle Lepersinus californicus Sw. (Coleoptera: Scolytidae) in North Dakota.

    PubMed

    Massey, C L

    1971-07-01

    Omemeea maxbassiensis n. gen., n. sp. was found inhabiting galleries of a bark beetle, Lepersinus californicus Sw., in green ash, Fraxinus pennsylvanica Marsh. The genus differs from all other genera in the subfamily in its uniquely shaped umbrella-like head, distinctive stylet, and location of excretory pore. PMID:19322384

  4. Omemeea maxbassiensis n. gen., n. sp. (Nematoda: Aphelenchoididae) from Galleries of the Bark Beetle Lepersinus californicus Sw. (Coleoptera: Scolytidae) in North Dakota

    PubMed Central

    Massey, C. L.

    1971-01-01

    Omemeea maxbassiensis n. gen., n. sp. was found inhabiting galleries of a bark beetle, Lepersinus californicus Sw., in green ash, Fraxinus pennsylvanica Marsh. The genus differs from all other genera in the subfamily in its uniquely shaped umbrella-like head, distinctive stylet, and location of excretory pore. PMID:19322384

  5. Poster Session--Predicting Patterns of Alien Plant Invasion--Underwood, Klinger, Moore USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 361

    E-print Network

    Standiford, Richard B.

    Poster Session--Predicting Patterns of Alien Plant Invasion--Underwood, Klinger, Moore USDA Forest Service Gen. Tech. Rep. PSW-GTR-189. 2008. 361 Predicting Patterns of Alien Plant Invasions in Areas of alien plant species. This is particularly problematic in areas which have experienced disturbances

  6. 147USDA Forest Service Gen. Tech. Rep. PSW-GTR-158. 1995. A Balanced Approach: Dr. Biswell's Solution to Fire Issues

    E-print Network

    Standiford, Richard B.

    147USDA Forest Service Gen. Tech. Rep. PSW-GTR-158. 1995. A Balanced Approach: Dr. Biswell's Solution to Fire Issues in Urban Interface and Wildland Ecosystems1 Carol Rice2 Abstract: Dr. Biswell's approach to fire management balanced fire prevention, suppression, and fuel management. Dr. Biswell

  7. CHROMOSOMAL MAPPING OF 12 GENE-ASSOCIATED MARKERS IN CATTLE IDENTIFIES NOVEL REGIONS OF CONSERVED SYNTENY BETWEEN THE HUMAN AND BOVINE GEN0MES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Current gene density on the bovine genetic maps is extremely limited and the resolution of the human-bovine comparative map is insufficient for selection of positional candidate genes controlling many economic traits of interest in dairy cattle. This study describes the chromosomal mapping of 12 gen...

  8. Wunderpus photogenicus n. gen. and sp., a new octopus from the shallow waters of the Indo-Malayan Archipelago (Cephalopoda: Octopodidae)

    Microsoft Academic Search

    F. G. HOCHBERG; MARK D. NORMAN; JULIAN FINN

    Wunderpus photogenicus n. gen. and n. sp. is a spectacular long-armed species that occurs on soft sediment habitats in shallow waters (typically less than 20 m deep) in Indo-Malayan waters. It is characterized by small eyes on elongate stalks, a long, conical papilla over each eye and a dramatic and fixed color pattern of white bars and spots over a

  9. Seismosaurus halli, gen. et sp. nov., a new sauropod dinosaur from the Morrison Formation (Upper Jurassic\\/Lower Cretaceous) of New Mexico, USA

    Microsoft Academic Search

    David D. Gillette

    1991-01-01

    Seismosaurus halli, gen. et sp. nov. (Sauropoda, Diplodocidae) is a new large sauropod from the Brushy Basin Member of the Morrison Formation (Upper Jurassic\\/Lower Cretaceous) of central New Mexico. The holotype is a partially articulated skeleton consisting to date of approximately 20 caudal vertebrae, five sacral vertebrae, eight dorsal vertebrae, partial pelvis, five chevrons, and ribs. Distinguishing features include the

  10. Evaluation of the Gen-Probe Aptima HIV-1 RNA Qualitative Assay as an Alternative to Western Blot Analysis for Confirmation of HIV Infection?

    PubMed Central

    Pierce, Virginia M.; Neide, Brandy; Hodinka, Richard L.

    2011-01-01

    The Gen-Probe Aptima HIV-1 RNA qualitative assay was evaluated as an alternative to Western blot analysis for the confirmation of HIV infection using serum samples that were repeatedly reactive for HIV antibodies. The Aptima HIV assay readily discriminated between HIV-1-infected and -uninfected individuals and effectively reduced the number of indeterminate results relative to Western blot analysis. PMID:21346052

  11. Appl Nbr Full TiFirst Name Middle Name Last Name Sex Category PH Category 00036777 F ADITI GUPTA F GEN N

    E-print Network

    Ribeiro, Vinay

    Appl Nbr Full TiFirst Name Middle Name Last Name Sex Category PH Category 00036777 F ADITI GUPTA F 00036674 F SRISHTI VIVEK SHARMA F GEN N Appl Nbr Full TiFirst Name Middle Name Last Name Sex Category PH) Appl Nbr Full TiFirst Name Middle Name Last Name Sex Category PH Category 00032299 F SANDEEP KUMAR

  12. Hardistiella montanensis n. gen. et sp. (Petromyzontida) from the Lower Carboniferous of Montana, with remarks on the affinities of the lampreys

    Microsoft Academic Search

    Philippe Janvier; Richard Lund

    1983-01-01

    Hardistiella montanensis n. gen. et sp. from the Lower Carboniferous (Namurian) Bear Gulch Limestone Member of the Heath Formation, Montana, is the only lamprey known to retain a clearly hypocercal tail and an anal fin provided with rays. These two characters are plesiomorphous and are also met with in “anaspids” and “thelodonts.” An analysis of the relationships of the petromyzontids

  13. 73USDAForestServiceGen.Tech.Rep.PSW-GTR-166.1998. Ozone concentrations have been monitored at the Glacier Lakes Ecosystem Experiment Site (GLEES) in the Snowy

    E-print Network

    Standiford, Richard B.

    with little diel variation in winter. Stratospheric intrusions contribute to the ground-level ozone73USDAForestServiceGen.Tech.Rep.PSW-GTR-166.1998. Abstract Ozone concentrations have been monitored of a mature subalpine forest near timberline. Continuous ozone and meteorological monitoring are a part

  14. Toxopsis calypsus gen. nov., sp. nov. (Cyanobacteria, Nostocales) from cave 'Francthi', Peloponnese, Greece: a morphological and molecular evaluation.

    PubMed

    Lamprinou, V; Skaraki, K; Kotoulas, G; Economou-Amilli, A; Pantazidou, A

    2012-12-01

    Representatives of a new cyanobacterial genus, Toxopsis Lamprinou & Pantazidou gen. nov., were found in fresh material from Cave 'Francthi' (Peloponnese, Greece) and isolated in cultures. Ecological data relating to the environmental parameters of the sampling sites are provided, such as the photosynthetically active radiation (PAR), temperature and relative humidity. Morphological characteristics and the life cycle of the type species Toxopsis calypsus Lamprinou & Pantazidou sp. nov. were studied using light microscopy and scanning and transmission microscopy. Molecular analysis based on the 16S rRNA gene sequence was also conducted. Toxopsis calypsus sp. nov. is a false-branched nostocalean cyanobacterium with both isopolar and heteropolar filaments bearing mono-pored and bi-pored heterocysts, and also hormogonia and akinetes. Isopolar filaments adhere by the centre to the substrate and are found mainly in fresh material and in young cultures; heteropolar filaments bearing a basic mono-pore heterocyst are dominant in aged (more than one-year-old) cultures. According to the revised taxonomic classification system of Komárek & Anagnostidis (1989) [Komárek, J. & Anagnostidis, K. (1989). Algol Stud, 56, 247-345] based mainly on morphological data, the new genus described here shares morphological characters with both nostocalean families Scytonemataceae and Microchaetaceae, showing similarities in particular to Scytonematopsis contorta [Vaccarino, M. A. & Johansen, J. R. (2011). Fottea 11, 149-161], Microchaetaceae. Molecular data from the 16S rRNA sequence determined in this paper showed that Toxopsis calypsus sp. nov. is more related to the family Microchaetaceae, and the five phylotypes analysed by PCR showed that the closest nostocalean relatives are Tolypothrix distorta SAG 93.79 (GenBank accession no. GQ287651) and Coleodesmium sp. ANT.L52B.5 (AY493596) with 95-96% and 96% similarity, respectively. In contrast, the five phylotypes showed a distant similarity to Scytonematopsis contorta (<91%). The phenotypic and genetic traits strongly supported the classification of the five phylotypes as a new taxon for which the name Toxopsis calypsus Lamprinou & Pantazidou gen. nov., sp. nov. is proposed. PMID:22247210

  15. Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces.

    PubMed

    Dridi, Bédis; Fardeau, Marie-Laure; Ollivier, Bernard; Raoult, Didier; Drancourt, Michel

    2012-08-01

    During attempts to obtain novel, human-associated species of the domain Archaea, a coccoid micro-organism, designated strain B10(T), was isolated in pure culture from a sample of human faeces collected in Marseille, France. On the basis of its phenotypic characteristics and 16S rRNA and mcrA gene sequences, the novel strain was classified as a methanogenic archaeon. Cells of the strain were non-motile, Gram-staining-positive cocci that were approximately 850 nm in diameter and showed autofluorescence at 420 nm. Cells were lysed by 0.1% (w/v) SDS. With hydrogen as the electron donor, strain B10(T) produced methane by reducing methanol. The novel strain was unable to produce methane when hydrogen or methanol was the sole energy source. In an atmosphere containing CO(2), strain B10(T) could not produce methane from formate, acetate, trimethylamine, 2-butanol, 2-propanol, cyclopentanol, 2-pentanol, ethanol, 1-propanol or 2,3-butanediol. Strain B10(T) grew optimally with 0.5-1.0% (w/v) NaCl, at pH 7.6 and at 37 °C. It required tungstate-selenite for growth. The complete genome of the novel strain was sequenced; the size of the genome was estimated to be 2.05 Mb and the genomic DNA G+C content was 59.93 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the highest sequence similarities (98.0-98.7%) were seen between strain B10(T) and several uncultured, methanogenic Archaea that had been collected from the digestive tracts of a cockroach, a chicken and mammals. In the same analysis, the non-methanogenic 'Candidatus Aciduliprofundum boonei' DSM 19572 was identified as the cultured micro-organism that was most closely related to strain B10(T) (83.0% 16S rRNA gene sequence similarity). Each of the three treeing algorithms used in the analysis of 16S rRNA gene sequences indicated that strain B10(T) belongs to a novel order that is distinct from the Thermoplasmatales. The novel strain also appeared to be distinct from Methanosphaera stadtmanae DSM 3091(T) (72.9% 16S rRNA gene sequence similarity), another methanogenic archaeon that was isolated from human faeces and can use methanol in the presence of hydrogen. Based on the genetic and phenotypic evidence, strain B10(T) represents a novel species of a new genus for which the name Methanomassiliicoccus luminyensis gen. nov., sp. nov. is proposed. The type strain of the type species is B10(T) (?=?DSM 24529(T)?=?CSUR P135(T)). PMID:22859731

  16. Characterization of some actinomyces-like isolates from human clinical sources: description of Varibaculum cambriensis gen nov, sp nov.

    PubMed

    Hall, Val; Collins, Matthew D; Lawson, Paul A; Hutson, Roger A; Falsen, Enevold; Inganas, Elisabeth; Duerden, Brian

    2003-02-01

    Fifteen strains of an anaerobic, catalase-negative, gram-positive diphtheroid-shaped bacterium recovered from human sources were characterized by phenotypic and molecular chemical and molecular genetic methods. The unidentified bacterium showed some resemblance to Actinomyces species and related taxa, but biochemical testing, polyacrylamide gel electrophoresis analysis of whole-cell proteins, and amplified 16S ribosomal DNA restriction analysis indicated the strains were distinct from all currently named Actinomyces species and related taxa. Comparative 16S rRNA gene sequencing studies showed that the bacterium represents a hitherto-unknown phylogenetic line that is related to but distinct from Actinomyces, Actinobaculum, Arcanobacterium, and Mobiluncus: We propose, on the basis of phenotypic and phylogenetic evidence, that the unknown bacterium from human clinical specimens should be classified as a new genus and species, Varibaculum cambriensis gen. nov., sp. nov. The type strain of Varibaculum cambriensis sp. nov. is CCUG 44998(T) = CIP 107344(T). PMID:12574260

  17. Characterization of Some Actinomyces-Like Isolates from Human Clinical Sources: Description of Varibaculum cambriensis gen. nov., sp. nov.

    PubMed Central

    Hall, Val; Collins, Matthew D.; Lawson, Paul A.; Hutson, Roger A.; Falsen, Enevold; Inganas, Elisabeth; Duerden, Brian

    2003-01-01

    Fifteen strains of an anaerobic, catalase-negative, gram-positive diphtheroid-shaped bacterium recovered from human sources were characterized by phenotypic and molecular chemical and molecular genetic methods. The unidentified bacterium showed some resemblance to Actinomyces species and related taxa, but biochemical testing, polyacrylamide gel electrophoresis analysis of whole-cell proteins, and amplified 16S ribosomal DNA restriction analysis indicated the strains were distinct from all currently named Actinomyces species and related taxa. Comparative 16S rRNA gene sequencing studies showed that the bacterium represents a hitherto-unknown phylogenetic line that is related to but distinct from Actinomyces, Actinobaculum, Arcanobacterium, and Mobiluncus. We propose, on the basis of phenotypic and phylogenetic evidence, that the unknown bacterium from human clinical specimens should be classified as a new genus and species, Varibaculum cambriensis gen. nov., sp. nov. The type strain of Varibaculum cambriensis sp. nov. is CCUG 44998T = CIP 107344T. PMID:12574260

  18. Dentiphilometra monopteri n. gen., n. sp. (Nematoda: Philometridae) from the abdominal cavity of the ricefield eel Monopterus albus in China.

    PubMed

    Moravec, Frantisek; Wang, Gui Tang

    2002-10-01

    A new genus and species of philometrid nematode Dentiphilometra monopteri n. gen., n. sp., are described on the basis of the specimens found in the abdominal cavity of the ricefield eel (swamp-eel) Monopterus albus (Zouiev) from Liangzi Lake (the Yangtze River drainage system), Hubei Province, in central China. Dentiphilometra, assigned to the Philometrinae, differs from other genera of this subfamily mainly in the presence of a sclerotized oral ring armed on its inner surface by numerous small peribuccal teeth in the gravid female. The new species is characterized by minute cephalic papillae, a greatly developed anterior esophageal bulb separated from the cylindrical part of the esophagus, anterior extention of the esophageal gland anterior to the nerve ring, and by large caudal projections in females and equal spicules 0.051-0.096 mm long in males. This is the second philometrid species recorded from fishes of the Synbranchiformes. PMID:12435137

  19. Tardiphaga robiniae gen. nov., sp. nov., a new genus in the family Bradyrhizobiaceae isolated from Robinia pseudoacacia in Flanders (Belgium).

    PubMed

    De Meyer, Sofie E; Coorevits, An; Willems, Anne

    2012-06-01

    Gram-negative, rod-shaped bacteria were isolated from Robinia pseudoacacia root nodules. On the basis of the 16S rRNA gene phylogeny, they are closely related to Bradyrhizobium, Rhodopseudomonas and Nitrobacter species (97% sequence similarity), belonging to the class Alphaproteobacteria and family Bradyrhizobiaceae. The results of physiological and biochemical tests together with sequence analysis of housekeeping genes (atpD, dnaK, gyrB, recA and rpoB) allowed differentiation of this group from other validly published Bradyrhizobiaceae genera. NodA, nodC and nifH genes could not be amplified. On the basis of genotypic and phenotypic data, these organisms represent a novel genus and species for which the name Tardiphaga robiniae gen. nov., sp. nov. (LMG 26467(T)=CCUG 61473(T)), is proposed. PMID:22444281

  20. Leptohelia flexibilis gen. nov. et sp. nov., a remarkable deep-sea stylasterid (Cnidaria: Hydrozoa: Stylasteridae) from the southwest Pacific.

    PubMed

    Lindner, Alberto; Cairns, Stephen D; Zibrowius, Helmut

    2014-01-01

    Leptohelia flexibilis gen. nov. et sp. nov., the first stylasterid with a combined calcified and non-calcified skeleton, is described from seamounts and the slope off the islands of New Caledonia, in the southwestern Pacific. The new species is distinguished from all other species of the family Stylasteridae by having a non-calcified organic axis, internal to the basal portion of the calcified corallum. The internal axis is flexible and enclosed by a series of up to 10 calcified annuli, allowing passive lateral bending of the colony. Molecular phylogenetic analyses confirm that Leptohelia flexibilis is a stylasterid coral and reveal that the species is closely related to Leptohelia microstylus comb. nov., a southwestern Pacific stylasterid that lacks an internal axis. PMID:25543758

  1. Third-Party Evaluation of Petro Tex Hydrocarbons, LLC, ReGen Lubricating Oil Re-refining Process

    SciTech Connect

    Compere, A L [ORNL; Griffith, William {Bill} L [ORNL

    2009-04-01

    This report presents an assessment of market, energy impact, and utility of the PetroTex Hydrocarbons, LLC., ReGen process for re-refining used lubricating oil to produce Group I, II, and III base oils, diesel fuel, and asphalt. PetroTex Hydrocarbons, LLC., has performed extensive pilot scale evaluations, computer simulations, and market studies of this process and is presently evaluating construction of a 23 million gallon per year industrial-scale plant. PetroTex has obtained a 30 acre site in the Texas Industries RailPark in Midlothian Texas. The environmental and civil engineering assessments of the site are completed, and the company has been granted a special use permit from the City of Midlothian and air emissions permits for the Texas Commission on Environmental Quality.

  2. Arnoldiellina fluorescens gen. et sp. nov.--a new green autofluorescent foraminifer from the Gulf of Eilat (Israel).

    PubMed

    Apothéloz-Perret-Gentil, Laure; Holzmann, Maria; Pawlowski, Jan

    2013-05-01

    A new monothalamous (single-chambered) soft-walled foraminiferal species, Arnoldiellina fluorescens gen. et sp. nov., was isolated from samples collected in the Gulf of Eilat, Israel. The species is characterized by a small elongate organic theca with a single aperture of allogromiids. It is characterized by the emission of green autofluorescence (GAF) that has so far not been reported from foraminifera. Phylogenetic analysis of a fragment of the 18S rDNA indicates that the species is related to a group of monothalamous foraminiferans classified as clade I. Although the morphology of the new species is very different compared to the other members of this clade, a specific helix in 18S rRNA secondary structure strongly supports this position. PMID:22999053

  3. Experimental Investigations of the Ablation of Wire Arrays on the 250 kA GenASIS Machine

    NASA Astrophysics Data System (ADS)

    Bott, S. C.; Haas, D. M.; Eshaq, Y.; Ueda, U.; Madden, R. E.; Collins, G.; Beg, F. N.

    2008-11-01

    We present investigations of exploding wire experiments on a recently completed linear transformer driver (LTD) in the High Energy Density Physics laboratory at UCSD. The GenASIS machine delivers >250kA in 130ns to short circuit and >200kA to a wire array load, via a conical constant gap power feed. Measured load currents compare favorably to circuit modeling. This new generator facilitates ablation studies of multiple wire cylindrical arrays with >25 kA/ wire, and we present laser Schlieren imaging, along with radial and axial electron density profiles inferred from interferometry for Al and W arrays, which are compared to analytical theory. In addition, conical wire arrays are used to generate supersonic plasma jets. We present characterization of high atomic number jets along with estimates of the local sound speed and Mach number.

  4. Comparison of Fracture Gradient Methods for the FutureGen 2.0 Carbon Storage Site, Ill., USA.

    NASA Astrophysics Data System (ADS)

    Appriou, D.; Spane, F.; Wurstner White, S.; Kelley, M. E.; Sullivan, E. C.; Bonneville, A.; Gilmore, T. J.

    2014-12-01

    As part of a first-of-its-kind carbon dioxide storage project, FutureGen Industrial Alliance is planning to inject 1.1 MMt/yr of supercritical CO2 over a 20-year period within a 1240 m deep saline aquifer (Mount Simon Sandstone) located in Morgan County, Illinois, USA. Numerous aspects of the design and operational activities of the CO2 storage site are dependent on the geomechanical properties of the targeted reservoir zone, as well as of the overlying confining zone and the underlying crystalline Precambrian basement. Detailed determination of the state-of-stress within the subsurface is of paramount importance in successfully designing well drilling/completion aspects, as well as assessing the risk of induced seismicity and the potential for creating and/or reopening pre-existing fractures; all of which help ensure the safe long-term storage of injected CO2. The quantitative determination of the subsurface fracture gradient is one of the key geomechanical parameters for the site injection design and operational limits (e.g., maximum safe injection pressure). A characterization well drilled in 2011 provides subsurface geomechanical characterization information for the FutureGen 2.0 site, and includes: 1) continuous elastic properties inferred from sonic/acoustic wireline logs 2) discrete depth geomechanical laboratory core measurements and 3) results obtained from hydraulic fracturing tests of selected borehole/depth-intervals. In this paper, the precise fracture gradients derived from borehole geomechanical test results are compared with semi-empirical, fracture gradient calculation/relationships based on elastic property wireline surveys and laboratory geomechanical core test results. Implications for using various fracture-gradients obtained from the different methods are assessed using PNNL's subsurface multiphase flow and transport simulator STOMP-CO2. The implications for operational activities at the site (based on using different fracture gradients) are also discussed.

  5. Enhanced/synthetic vision and head-worn display technologies for terminal maneuvering area NextGen operations

    NASA Astrophysics Data System (ADS)

    Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Williams, Steven P.; Bailey, Randall E.; Shelton, Kevin J.; Norman, R. Mike

    2011-06-01

    NASA is researching innovative technologies for the Next Generation Air Transportation System (NextGen) to provide a "Better-Than-Visual" (BTV) capability as adjunct to "Equivalent Visual Operations" (EVO); that is, airport throughputs equivalent to that normally achieved during Visual Flight Rules (VFR) operations rates with equivalent and better safety in all weather and visibility conditions including Instrument Meteorological Conditions (IMC). These new technologies build on proven flight deck systems and leverage synthetic and enhanced vision systems. Two piloted simulation studies were conducted to access the use of a Head-Worn Display (HWD) with head tracking for synthetic and enhanced vision systems concepts. The first experiment evaluated the use a HWD for equivalent visual operations to San Francisco International Airport (airport identifier: KSFO) compared to a visual concept and a head-down display concept. A second experiment evaluated symbology variations under different visibility conditions using a HWD during taxi operations at Chicago O'Hare airport (airport identifier: KORD). Two experiments were conducted, one in a simulated San Francisco airport (KSFO) approach operation and the other, in simulated Chicago O'Hare surface operations, evaluating enhanced/synthetic vision and head-worn display technologies for NextGen operations. While flying a closely-spaced parallel approach to KSFO, pilots rated the HWD, under low-visibility conditions, equivalent to the out-the-window condition, under unlimited visibility, in terms of situational awareness (SA) and mental workload compared to a head-down enhanced vision system. There were no differences between the 3 display concepts in terms of traffic spacing and distance and the pilot decision-making to land or go-around. For the KORD experiment, the visibility condition was not a factor in pilot's rating of clutter effects from symbology. Several concepts for enhanced implementations of an unlimited field-of-regard BTV concept for low-visibility surface operations were determined to be equivalent in pilot ratings of efficacy and usability.

  6. GenLab: A MATLAB ®-based program for structural analysis of folds mapped by GPS or seismic methods

    NASA Astrophysics Data System (ADS)

    Fernández-Martínez, J. L.; Lisle, Richard J.

    2009-02-01

    GenLab is a MATLAB ® code for structural analysis of digitally and seismically mapped horizons based on the geometrical model of the developable surface. This model is chosen because surfaces of this type result from the bending of a non-stretching stratum and because deviation from developable geometry implies that bed stretching during folding has occurred. The model is therefore linked with straining of the horizon and can be used for highlighting regions of deformation expressed by brittle fracturing or ductile deformation. Mathematically, a developable surface is one upon which straight lines (generators) can be drawn, and along these generators the orientations of tangent planes of the surface remain constant. Our method involves treating real geological surfaces as approximations to developable surfaces and determines the generator lines at different points on the surface. At these points we consider strip samples of the surface radiating in different directions and examine the variability of strike and dip within each sample strip. The radial scan-line length parameter is user-defined, and the optimal value can be easily identified by geostatistical analysis of the depth data. The local plunge lines (the approximation to the generatrix of a developable fold) are therefore identified as the direction associated with the least variation of surface attitude, i.e., the most constant strike and dip. The map pattern obtained by analyzing the plunges and trends of plunge lines across an area allows identification of domains where folding accords closely with a developable geometry. Such domains are recognized from straight plunge lines, defining parallel or convergent patterns. According to the model, deviations from these patterns correspond to regions of structural complexity associated with ductile or brittle straining of the surface being analyzed. The plunge-line analysis therefore offers a useful technique with potential for predicting strained zones and automatic fault recognition. GenLab allows the rapid implementation of this analysis and uses the matrix capabilities and contouring functions of MATLAB.

  7. Abstract. The contentious and litigious history associated with managing Northern Goshawks (Accipiter gen-tilis) has focused much research attention toward understanding this species' life history. Results from these

    E-print Network

    Words: Accipiter gentilis, goshawk ecology, goshawk management, Northern Goshawk. ECOLOGÍA DEL GAVILÁN (Accipiter gen- tilis) has focused much research attention toward understanding this species' life history CONSERVACIÓN Resumen. La contenciosa y discordante historia asociada al manejo del Gavilán Azor (Accipiter

  8. A new remarkable subterranean beetle of the Rhodopes: Paralovricia gen. n. beroni sp. n. belonging to Lovriciina new subtribe (Coleoptera, Carabidae, Trechinae, Bembidiini)

    PubMed Central

    Giachino, Pier Mauro; Guéorguiev, Borislav; Vailati, Dante

    2011-01-01

    Abstract Paralovricia gen. n. beroni sp. n., belonging to the new subtribe Lovriciina, is described from two caves in the Western Rhodopes (Bulgaria): Kraypatnata peshtera, near Smilyan Village (Smolyan Municipality) and Snezhanka, near Peshtera Town (Peshtera Municipality). Three currently known genera, Lovricia Pretner, 1979, Neolovricia Lakota, Jalži? & Moravec, 2009 and Paralovricia gen. n. represent a monophyletic unit supported by important synapomorphies that allows to propose the establishment of the new subtribe Lovriciina, characterized by the following characters: last maxillary palpomeres very long and narrow, basal angles of pronotum without seta, elytra without discal setae, elytral umbilicate series of nine pores in which the main pores are the 2nd, 6th and 9th, apical recurrent striole absent and mesotibial apex expanded outward. Its systematic position within the subfamily Trechinae (sensu Lorenz 2005) is discussed and Lovriciina is placed near Anillina. Key to the genera of the subtribe is proposed. Distribution data and zoogeographical hypotheses are discussed. PMID:21998506

  9. A review of "The Variorum Edition of the Poetry of John Donne: The Holy Sonnets." by Gary A. Stringer gen. ed.

    E-print Network

    Albert C. Labriola

    2006-01-01

    REVIEWS 1 Gary A. Stringer, gen. ed. The Variorum Edition of the Poetry of John Donne: The Holy Sonnets, Volume 7, Part 1. Bloomington: Indiana University Press, 2005. cvii + 606 pp. $59.95. Review by ALBERT C. LABRIOLA, DUQUESNE UNIVERSITY... designated ?An Approved Edition,? excels beyond our highest expectations. First and foremost, the volume interrelates textual study and critical com- mentary in the most effective ways. The editors, in fact, organize their textual study to accord with many...

  10. INSTITUTE OF PHYSICS PUBLISHING JOURNAL OF PHYSICS A: MATHEMATICAL AND GENERAL J. Phys. A: Math. Gen. 39 (2006) 22872306 doi:10.1088/0305-4470/39/10/004

    E-print Network

    Cohen, Doron

    2006-01-01

    . Gen. 39 (2006) 2287­2306 doi:10.1088/0305-4470/39/10/004 Quantum stirring of particles in closed at stacks.iop.org/JPhysA/39/2287 Abstract We study the quantum analogue of stirring of water inside a cup. A 0305-4470/06/102287+20$30.00 © 2006 IOP Publishing Ltd Printed in the UK 2287 #12;2288 G Rosenberg

  11. Intraspecific Variation in Small-Subunit rRNA Sequences in GenBank: Why Single Sequences May Not Adequately Represent Prokaryotic Taxa

    Microsoft Academic Search

    REBECCA A. CLAYTON; GRANGER SUTTON; PAUL S. HINKLE; CAROL BULT

    Small-subunit rRNA (SSU rRNA) sequencing is a powerful tool to detect, identify, and classify prokaryotic organisms, and there is currently an explosion of SSU rRNA sequencing in the microbiology community. We report unexpectedly high levels of intraspecific variation (within and between strains) of prokaryote SSU rRNA sequences deposited in GenBank. A total of 82% of the prokaryote species with two

  12. A new African soft scale genus, Pseudocribrolecanium gen. nov. (Hemiptera: Coccoidea: Coccidae), erected for two species, including the citrus pest P. andersoni (Newstead) comb. nov

    PubMed Central

    Kondo, Takumasa

    2006-01-01

    A new African genus of soft scale insects, Pseudocribrolecanium gen. nov. is erected to accommodate Akermes colae Green & Laing and Cribrolecanium andersoni (Newstead). The adult females and first-instar nymphs of the two species are redescribed and illustrated. Taxonomic keys to separate the adult females and first-instar nymphs are provided. The affinity of Pseudocribrolecanium with the tribe Paralecaniini in the subfamily Coccinae is discussed. PMID:19537997

  13. AtGEN1 and AtSEND1, Two Paralogs in Arabidopsis, Possess Holliday Junction Resolvase Activity1[W][OPEN

    PubMed Central

    Bauknecht, Markus; Kobbe, Daniela

    2014-01-01

    Holliday junctions (HJs) are physical links between homologous DNA molecules that arise as central intermediary structures during homologous recombination and repair in meiotic and somatic cells. It is necessary for these structures to be resolved to ensure correct chromosome segregation and other functions. In eukaryotes, including plants, homologs of a gene called XPG-like endonuclease1 (GEN1) have been identified that process HJs in a manner analogous to the HJ resolvases of phages, archaea, and bacteria. Here, we report that Arabidopsis (Arabidopsis thaliana), a eukaryotic organism, has two functional GEN1 homologs instead of one. Like all known eukaryotic resolvases, AtGEN1 and Arabidopsis single-strand DNA endonuclease1 both belong to class IV of the Rad2/XPG family of nucleases. Their resolvase activity shares the characteristics of the Escherichia coli radiation and UV sensitive C paradigm for resolvases, which involves resolving HJs by symmetrically oriented incisions in two opposing strands. This leads to ligatable products without the need for further processing. The observation that the sequence context influences the cleavage by the enzymes can be interpreted as a hint for the existence of sequence specificity. The two Arabidopsis paralogs differ in their preferred sequences. The precise cleavage positions observed for the resolution of mobile nicked HJs suggest that these cleavage positions are determined by both the substrate structure and the sequence context at the junction point. PMID:25037209

  14. GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing

    PubMed Central

    2010-01-01

    Background Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis is thus essential to our understanding of how selective and neutral forces shape bacterial populations over a short period of time. The Solexa Genome Analyzer, a next-generation sequencing platform, allows millions of short sequencing reads to be obtained with great accuracy, allowing for the ability to study the dynamics of the bacterial population at the whole genome level. The tool referred to as GenHtr was developed for genome-wide heterogeneity analysis. Results For particular bacterial strains, GenHtr relies on a set of Solexa short reads on given bacteria pathogens and their isogenic reference genome to identify heterogeneity sites, the chromosomal positions with multiple variants of genes in the bacterial population, and variations that occur in large gene families. GenHtr accomplishes this by building and comparatively analyzing genome-wide heterogeneity genotypes for both the newly sequenced genomes (using massive short-read sequencing) and their isogenic reference (using simulated data). As proof of the concept, this approach was applied to SRX007711, the Solexa sequencing data for a newly sequenced Staphylococcus aureus subsp. USA300 cell line, and demonstrated that it could predict such multiple variants. They include multiple variants of genes critical in pathogenesis, e.g. genes encoding a LysR family transcriptional regulator, 23 S ribosomal RNA, and DNA mismatch repair protein MutS. The heterogeneity results in non-synonymous and nonsense mutations, leading to truncated proteins for both LysR and MutS. Conclusion GenHtr was developed for genome-wide heterogeneity analysis. Although it is much more time-consuming when compared to Maq, a popular tool for SNP analysis, GenHtr is able to predict potential multiple variants that pre-exist in the bacterial population as well as SNPs that occur in the highly duplicated gene families. It is expected that, with the proper experimental design, this analysis can improve our understanding of the molecular mechanism underlying the dynamics and the evolution of drug-resistant bacterial pathogens. PMID:20939910

  15. New SSU-rDNA sequences for eleven colpodeans (Ciliophora, Colpodea) and description of Apocyrtolophosis nov. gen.

    PubMed

    Foissner, Wilhelm; Bourland, William A; Wolf, Klaus W; Stoeck, Thorsten; Dunthorn, Micah

    2014-02-01

    Using 11 new SSU-rDNA sequences, we analyze relationships within the class Colpodea, especially of some uncommon taxa, such as Kalometopia duplicata, Cyrtolophosis minor, and Jaroschia sumptuosa. The sequences do not change the basic structure of the molecular Colpodea tree, i.e., all belong to one of the four molecular clades recognized by Foissner et al. (2011): Colpodida, Cyrtolophosidida, Bursariomorphida, and Platyophryida. The addition of three Colpoda sequences strengthens the observation that species of this genus are distributed over the whole molecular Colpodea tree. Very likely, this is caused by a fast radiation of Colpoda, several species of which then evolved independently, forming new genera and families. Cyrtolophosis minor, which belongs to the molecular Pseudocyrtolophosis clade, is referred to a new genus, Apocyrtolophosis nov. gen., characterized by a comparably large, deltoid oral opening, an unciliated posterior region, and the absence of an oblique kinety in the left oral polykinetid. Bryometopus triquetrus does not erase the paraphyly of its genus. Platyophrya vorax, P. spumacola, and P. bromelicola form a highly supported clade in the order Platyophryida. Platyophryides and Ottowphrya are close genetically but differ in the silverline pattern (colpodid vs. platyophryid). PMID:24210999

  16. Iamia majanohamensis gen. nov., sp. nov., an actinobacterium isolated from sea cucumber Holothuria edulis, and proposal of Iamiaceae fam. nov.

    PubMed

    Kurahashi, Midori; Fukunaga, Yukiyo; Sakiyama, Yayoi; Harayama, Shigeaki; Yokota, Akira

    2009-04-01

    A novel, Gram-positive bacterial strain, F12(T), was isolated from the abdominal epidermis of a sea cucumber, Holothuria edulis, collected from seawater off the coast of Japan. According to 16S rRNA gene sequence analysis, this strain represents a novel, deep-rooting lineage within the class Actinobacteria and clusters with uncultured bacteria and Acidimicrobium ferrooxidans. Compared to species with validly published names, the highest 16S rRNA gene sequence similarity (89.8 %) was to Acidimicrobium ferrooxidans DSM 10331(T). Phylogenetic analyses showed that strain F12(T) represents a distinct phylogenetic lineage related closely to the genus Acidimicrobium. Strain F12(T) contained MK-9(H(6)) as the major menaquinone, whilst 17 : 0, 17 : 1omega8c, 15 : 0 and 16 : 0 were the major cellular fatty acids. The cell-wall peptidoglycan of strain F12(T) was composed of meso-diaminopimelic acid as the diagnostic diamino acid, alanine and glutamic acid (1 : 2 : 1). The cell-wall sugars detected were rhamnose, mannose, arabinose, galactose and xylose. The G+C content of the DNA was 74.4 mol%. From the taxonomic data obtained in this study, the name Iamia majanohamensis gen. nov., sp. nov. is proposed for the isolate, with type strain F12(T) (=NBRC 102561(T)=DSM 19957(T)). The name Iamiaceae fam. nov. is also proposed for the distinct phyletic line represented by the genus Iamia. PMID:19329622

  17. Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum 'Verrucomicrobia' isolated from seawater in Japan.

    PubMed

    Yoon, Jaewoo; Yasumoto-Hirose, Mina; Katsuta, Atsuko; Sekiguchi, Hiroshi; Matsuda, Satoru; Kasai, Hiroaki; Yokota, Akira

    2007-05-01

    An obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium, designated strain 04OKA010-24(T), was isolated from seawater surrounding the hard coral Galaxea fascicularis L., collected at Majanohama, Akajima, Japan, and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain represented a member of the phylum 'Verrucomicrobia' and shared 84-95 % sequence similarity with cultivated strains of 'Verrucomicrobia' subdivision 4. Amino acid analysis of the cell-wall hydrolysate indicated the absence of muramic acid and diaminopimelic acid, which suggested that the strain did not contain peptidoglycan in the cell wall. The G+C content of the DNA was 53.9 mol%. MK-7 was the major menaquinone and C(14 : 0), C(18 : 1)omega9c and C(18 : 0) were the major fatty acids. On the basis of these data, it was concluded that strain 04OKA010-24(T) represents a novel species in a new genus in subdivision 4 of the phylum 'Verrucomicrobia', for which the name Coraliomargarita akajimensis gen. nov., sp. nov. is proposed. The type strain of Coraliomargarita akajimensis is 04OKA010-24(T) (=MBIC06463(T)=IAM 15411(T)=KCTC 12865(T)). PMID:17473241

  18. Persicitalea jodogahamensis gen. nov., sp. nov., a marine bacterium of the family 'Flexibacteraceae', isolated from seawater in Japan.

    PubMed

    Yoon, Jaewoo; Ishikawa, Shu; Kasai, Hiroaki; Yokota, Akira

    2007-05-01

    An obligately aerobic, Gram-negative, non-motile, pale-pink-pigmented, rod-shaped strain, designated Shu-9-SY12-35C(T), was isolated from seawater in Jodogahama, Iwate, Japan, and was subjected to a polyphasic taxonomic examination. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family 'Flexibacteraceae' of the phylum Bacteroidetes and that it showed highest sequence similarity (86.4 %) with Dyadobacter hamtensis HHS 11(T). The novel isolate is phenotypically and physiologically different from strains described previously. The G+C content of the DNA was 56.3 mol%, MK-7 was the major menaquinone and iso-C(15 : 0), C(16 : 1)omega7c and iso-C(17 : 0) 3-OH were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain Shu-9-SY12-35C(T) represents a new genus and species of the family 'Flexibacteraceae', for which the name Persicitalea jodogahamensis gen. nov., sp. nov. is proposed. The type strain of Persicitalea jodogahamensis is Shu-9-SY12-35C(T) (=MBIC07417(T)=IAM 15412(T)=KCTC 12866(T)). PMID:17473250

  19. Limibacter armeniacum gen. nov., sp. nov., a novel representative of the family 'Flammeovirgaceae' isolated from marine sediment.

    PubMed

    Yoon, Jaewoo; Matsuo, Yoshihide; Kasai, Hiroaki; Yokota, Akira

    2008-04-01

    Two strictly aerobic, Gram-negative, gliding, apricot- to pale-orange-pigmented, rod-shaped bacteria, strains YM11-185T and YM11-159, were isolated from marine sediments in the Republic of Palau. Preliminary analysis based on the 16S rRNA gene sequence revealed that the novel isolates could be affiliated with the family 'Flammeovirgaceae' of the phylum Bacteroidetes. Strains YM11-185T and YM11-159 shared 100 % sequence similarity and showed less than 90 % similarity to cultivated representatives of the family 'Flammeovirgaceae'. The novel isolates are phenotypically and physiologically different from strains described previously. The G+C content of DNA was 27.8-27.9 mol%, MK-7 was the major menaquinone and iso-C15 : 0 and C16 : 1 omega 7c were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strains YM11-185T and YM11-159 represent a novel species in a new genus of the family 'Flammeovirgaceae', for which the name Limibacter armeniacum gen. nov., sp. nov. is proposed. The type strain of Limibacter armeniacum is YM11-185T (=MBIC08286T =KCTC 22132T). PMID:18398206

  20. Portibacter lacus gen. nov., sp.nov., a new member of the family Saprospiraceae isolated from a saline lake.

    PubMed

    Yoon, Jaewoo; Matsuo, Yoshihide; Kasai, Hiroaki; Yokota, Akira

    2012-01-01

    A strictly aerobic, Gram-negative, orange-pigmented, rod-shaped, non-motile and chemoheterotrophic bacteria representing a new genus and species, designated YM8-076T, was isolated from lake water collected at a harbor on Lake Notoro, Hokkaido, Japan. Preliminary analysis based on the 16S rRNA gene sequence revealed that the novel isolate could be affiliated with the family Saprospiraceae of the phylum Bacteroidetes and that it showed highest sequence similarity (88.5%) to Haliscomenobacter hydrossis ATCC 27775T. The strain could be differentiated phenotypically from recognized members of the family Saprospiraceae. The G+C content of DNA was 53.7 mol%, MK-7 was the major menaquinone and iso-C15?0, iso-C15?1 and iso-C17?0 3-OH were the major cellular fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain YM8-076T represents a new genus and species of the family Saprospiraceae. We propose the name Portibacter lacus gen. nov., sp. nov. for this strain; its type strain is YM8-076T (=KCTC 23747T=NBRC 108769T). PMID:22878737

  1. Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov., thermophilic anaerobic representatives of the phylum Planctomycetes.

    PubMed

    Slobodkina, Galina B; Kovaleva, Olga L; Miroshnichenko, Margarita L; Slobodkin, Alexander I; Kolganova, Tatyana V; Novikov, Andrei A; van Heerden, Esta; Bonch-Osmolovskaya, Elizaveta A

    2015-03-01

    Two novel strains of thermophilic planctomycetes were recovered from terrestrial and subterranean habitats. Strain R1(T) was isolated from a hot spring (Kunashir Island, Russia) and strain SBP2(T) was isolated from a deep gold mine (South Africa). Both isolates grew in the temperature range 30-60 °C and pH range 5.0-8.0. Strain R1(T) grew optimally at 60 °C and pH 6.0-6.5; for SBP2(T) optimal conditions were at 52 °C and pH 7.5-8.0. Both strains were capable of anaerobic respiration with nitrate and nitrite as electron acceptors as well as of microaerobic growth. They also could grow by fermentation of mono-, di- and polysaccharides. Based on their phylogenetic position and phenotypic features we suggest that the new isolates represent two novel species belonging to a new genus in the order Planctomycetales, for which the names Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov. are proposed. The type strain of Thermogutta terrifontis, the type species of the genus, is R1(T) (?=?DSM 26237(T)?=?VKM B-2805(T)), and the type strain of Thermogutta hypogea is SBP2(T) (?=?JCM 19991(T)?=?VKM B-2782(T)). PMID:25479950

  2. Aureisphaera galaxeae gen. nov., sp. nov., a marine member of the family Flavobacteriaceae isolated from the hard coral Galaxea fascicularis.

    PubMed

    Yoon, Jaewoo; Yasumoto-Hirose, Mina; Kasai, Hiroaki

    2015-06-01

    A novel Gram-stain negative, spherical, non-motile, strictly aerobic, heterotrophic, yellow pigmented bacterium, designated strain 04OKA003-7(T) was isolated from the hard coral Galaxea fascicularis L. collected at Akajima, Okinawa, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (92.9 %) to Vitellibacter aestuarii JC2436(T) and Aureitalea marina S1-66(T). The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain 04OKA003-7(T) were identified as iso-C15:0 and iso-C17:0 3-OH as defined by the MIDI system. The DNA G+C content was determined to be 41 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Aureisphaera galaxeae gen. nov., sp. nov. is proposed. The type strain of A. galaxeae is 04OKA003-7(T) (=KCTC 32993(T) = NBRC 110018(T)). PMID:25795444

  3. Revision of the Genus Coriplites Foissner, 1988 (Ciliophora: Haptorida), with Description of Apocoriplites nov. gen. and Three New Species

    PubMed Central

    OERTEL, Anke; WOLF, Klaus; AL-RASHEID, Khaled; FOISSNER, Wilhelm

    2010-01-01

    Summary The genera Coriplites Foissner, 1988 and Apocoriplites nov. gen., which differ by the number of dorsal brush rows (3 vs. 2), belong to the haptorid Litostomatea and have a distinct feature in common: they lack oral extrusomes. Based on three new species, the diagnosis of the genus Coriplites is amended to include the wide spacing of the brush dikinetids and the heavily refractive cortical granules. Using standard methods, we redescribe C. terricola Foissner, 1988 and describe three new species: C. grandis (from swamp soil of Australia), C. proctori (from tanks of bromeliads in Jamaica), and Apocoriplites lajacola (from granitic rook-pools in Venezuela). Species are distinguished by the nuclear apparatus (a single nodule vs. two nodules with a micronucleus in between), the body size (<100 ?m vs. >100 ?m), the number of ciliary rows, and details of the dorsal brush (isostichad vs. heterostichad). In over 1,000 soil samples, only C. terricola has been found in all main biogeographic regions, while the other species have been found only at their type locality, i.e., in the southern hemisphere, where the genus possibly originated. PMID:20622920

  4. Vulcanibacillus modesticaldus gen. nov., sp. nov., a strictly anaerobic, nitrate-reducing bacterium from deep-sea hydrothermal vents.

    PubMed

    L'Haridon, S; Miroshnichenko, M L; Kostrikina, N A; Tindall, B J; Spring, S; Schumann, P; Stackebrandt, E; Bonch-Osmolovskaya, E A; Jeanthon, C

    2006-05-01

    A novel anaerobic, moderately thermophilic, spore-forming bacterium, designated strain BRT, was isolated from deep-sea hydrothermal core samples collected at the Rainbow vent field on the Mid-Atlantic Ridge (36 degrees 14' N 33 degrees 54' W). The cells were found to be rod-shaped, non-motile, Gram-positive and spore-forming. The organism grew in the temperature range 37-60 degrees C, with an optimum at 55 degrees C, and at pH values in the range 6-8.5, with an optimum around pH 7. NaCl concentrations for growth were in the range 10-40 g l(-1), with an optimum at 20-30 g l(-1). Strain BRT grew chemo-organoheterotrophically with carbohydrates, proteinaceous substrates and organic acids with nitrate as electron acceptor. The novel isolate was not able to ferment. The G+C content of the genomic DNA was 34.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain BRT in the Bacillaceae within the class 'Bacilli'. On the basis of the phenotypic and phylogenetic data, this isolate should be described as a member of a novel genus, for which the name Vulcanibacillus gen. nov. is proposed. The type species is Vulcanibacillus modesticaldus sp. nov., with the type strain BRT (=DSM 14931T=JCM 12998T). PMID:16627653

  5. Isolation and characterization of Keratinibaculum paraultunense gen. nov., sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity.

    PubMed

    Huang, Yan; Sun, Yingjie; Ma, Shichun; Chen, Lu; Zhang, Hui; Deng, Yu

    2013-08-01

    A novel thermophilic, anaerobic, keratinolytic bacterium designated KD-1 was isolated from grassy marshland. Strain KD-1 was a spore-forming rod with a Gram-positive type cell wall, but stained Gram-negative. The temperature, pH, and NaCl concentration range necessary for growth was 30-65 °C (optimum 55 °C), 6.0-10.5 (optimum 8.0-8.5), and 0-6% (optimum 0.2%) (w/v), respectively. Strain KD-1 possessed extracellular keratinase, and the optimum activity of the crude enzyme was pH 8.5 and 70 °C. The enzyme was identified as a thermostable serine-type protease. The strain was sensitive to rifampin, chloramphenicol, kanamycin, and tetracycline and was resistant to erythromycin, neomycin, penicillin, and streptomycin. The main cellular fatty acid was predominantly C15:0 iso (64%), and the G+C content was 28 mol%. Morphological and physiological characterization, together with phylogenetic analysis based on 16S rRNA gene sequencing identified KD-1 as a new species of a novel genus of Clostridiaceae with 95.3%, 93.8% 16S rRNA gene sequence similarity to Clostridium ultunense BS(T) (DSM 10521(T)) and Tepidimicrobium xylanilyticum PML14(T) (= JCM 15035(T)), respectively. We propose the name Keratinibaculum paraultunense gen. nov., sp. nov., with KD-1 (=JCM 18769(T) =DSM 26752(T)) as the type strain. PMID:23710623

  6. Value of a DNA probe assay (Gen-Probe) compared with that of culture for diagnosis of gonococcal infection.

    PubMed Central

    Vlaspolder, F; Mutsaers, J A; Blog, F; Notowicz, A

    1993-01-01

    The Gen-Probe PACE 2 system for Neisseria gonorrhoeae (GP), which uses a chemiluminescently labeled DNA probe, was compared with conventional culture as the method of reference. A total of 1,750 specimens were collected from 496 females and 623 males visiting the outpatient clinic of the Sexually Transmitted Diseases Department of the Westeinde Hospital, The Hague, The Netherlands, during the year 1991. The prevalences of gonorrhea culture-positive men and women were 14.9 and 7.7%, respectively. The overall positive rate was 8.7%. Sensitivity, specificity, and positive and negative predictive values of GP were 97.1, 99.1, 90.6, and 99.8%, respectively. A total of 12 of 13 patients with positive GP results and negative cultures may have had a gonococcal infection, a conclusion based on clinical symptoms, positive methylene blue smears, and high relative light unit ratios. The DNA probe test can be useful as a suitable screening and diagnostic test for gonorrheal infection in men and women. An advantage of using this DNA probe technique is that simultaneous testing for Chlamydia trachomatis of the same specimen is possible. We also examined whether (all) rRNA had disappeared after adequate treatment for gonococcal and/or chlamydial infection in 30 patients. None of those positive patients showed a positive result in the DNA probe assay after treatment. PMID:8417014

  7. Caldisphaera lagunensis gen. nov., sp. nov., a novel thermoacidophilic crenarchaeote isolated from a hot spring at Mt Maquiling, Philippines.

    PubMed

    Itoh, T; Suzuki, K; Sanchez, P C; Nakase, T

    2003-07-01

    Four novel, thermoacidophilic, crenarchaeotic cocci that grew anaerobically and heterotrophically were isolated from an acidic hot spring in the Philippines; two representative strains were characterized in detail. Most cells were regular cocci, 0.8-1.1 microm in width, which occurred singly or in pairs. They were non-motile and grew at 45-80 degrees C (optimum 70-75 degrees C) and pH 2.3-5.4 (optimum 3.5-4.0). They utilized starch, glycogen, gelatin, beef extract, yeast extract and peptone as carbon and energy sources. Growth was stimulated by the presence of sulfur as an electron acceptor. The lipid fraction contained cyclic and acyclic tetraether core lipids. The DNA G + C content was 31 mol%; phylogenetic analysis based on 16S rDNA sequences showed that the novel cocci represent an independent lineage in the phylum Crenarchaeota, distantly related to Acidilobus aceticus and an allied strain, NC12. Caldisphaera lagunensis gen. nov., sp. nov. is proposed to accommodate the four strains. The type strain is IC-154T (=JCM 11604T=MCC-UPLB 1331T=ANMR 0165T). PMID:12892143

  8. A haptophyte bearing siliceous scales: ultrastructure and phylogenetic position of Hyalolithus neolepis gen. et sp. nov. (Prymnesiophyceae, Haptophyta).

    PubMed

    Yoshida, Masaki; Noël, Mary-Hélène; Nakayama, Takeshi; Naganuma, Takeshi; Inouye, Isao

    2006-06-01

    A haptophyte alga bearing hyaline but conspicuous scales was discovered in surface water samples of Shiribeshi Seamount, Japan. X-ray elemental analysis confirmed that silica was the major element in these scales. These scales were hat-shaped, ellipsoidal in top view, 4-6mum wide and 5-7mum long, perforated by several small pores, and were deposited on cells in several layers. Beneath the siliceous scale layers, organic scales were present, which are typical of haptophytes. The cells were non-motile despite having two short flagella hidden in the scale case. The haptonema, extended over the scale case, and one and a half times the cell length. The intracellular features were typical of haptophytes, including the peripheral endoplasmic reticulum (PER), Golgi cisternae with peculiar dilations, and the flagellar apparatus. The siliceous scales were produced in vesicles in the posterior region of the cell. Motile cells lacking silica scales were observed occasionally when cultures were maintained at lower temperatures and under oligotrophic conditions. This alga was described as Hyalolithus neolepis gen. et sp. nov. Phylogenetic analysis using the SSU rDNA and rbcL gene sequences indicated that Hyalolithus is a member of the Prymnesiales and falls in a clade including Prymnesium, Platychrysis, and Chrysochromulina polylepis. Based on these results, the evolutionary implications of the presence of silicified scales in haptophytes is discussed. PMID:16647294

  9. Alkalibaculum bacchi gen. nov., sp. nov., a CO-oxidizing, ethanol-producing acetogen isolated from livestock-impacted soil.

    PubMed

    Allen, Toby D; Caldwell, Matthew E; Lawson, Paul A; Huhnke, Raymond L; Tanner, Ralph S

    2010-10-01

    Phenotypic and phylogenetic studies were performed on three strains of an acetogenic bacterium isolated from livestock-impacted soil. The bacterium stained Gram-negative and was a non-spore-forming rod that was motile by peritrichous flagella. The novel strains had an optimum pH for growth of 8.0-8.5 and utilized H??:?CO?, CO?:?CO?, glucose, fructose, mannose, turanose, ribose, trimethylamine, pyruvate, methanol, ethanol, n-propanol and n-butanol as growth substrates. Acetate was produced from glucose. Acetate, CO? and ethanol were produced from CO?:?CO?. 16S rRNA gene sequence analysis indicated that the novel strains formed a new subline in the family Eubacteriaceae (rRNA cluster XV) of the low G+C-containing Gram-positive bacteria of the class Clostridia. The DNA G+C base composition was 34 mol%. Cell wall analysis revealed the existence of a novel B-type peptidoglycan similar to the B2?-type (B4) configuration with a variation containing aspartic acid. Based on phylogenetic and phenotypic evidence, it is proposed that the new isolates represent a novel genus and species, for which the name Alkalibaculum bacchi gen. nov., sp. nov. is proposed. The type strain of the type species is CP11(T) (=ATCC BAA-1772(T)=DSM 22112(T)). PMID:19965999

  10. Imperialibacter roseus gen. nov., sp. nov., a novel bacterium of the family Flammeovirgaceae isolated from Permian groundwater.

    PubMed

    Wang, Hui; Li, Junde; Zheng, Tianling; Hill, Russell T; Hu, Xiaoke

    2013-11-01

    A novel bacterial strain, designated P4(T), was isolated from Permian groundwater and identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics. Cells were aerobic, Gram-stain-negative rods. 16S rRNA gene sequence-based phylogenetic analysis revealed that P4(T) is affiliated with the family Flammeovirgaceae in the phylum Bacteroidetes, but forms a distinct cluster within this family. The DNA G+C content of strain P4(T) was 45.2 mol%. The predominant cellular fatty acids were C16?:?1?6c/C16?:?1?7c and iso-C15?:?0. MK-7 was the main respiratory quinone. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid, unidentified glycolipids and unidentified polar lipids. Based on our extensive polyphasic analysis, a novel species in a new genus, Imperialibacter roseus gen. nov., sp. nov., is proposed. The type strain of Imperialibacter roseus is P4(T) (?=?CICC 10659(T)?=?KCTC 32399(T)). PMID:23749281

  11. Factors Influencing the Decisions and Actions of Pilots and Air Traffic Controllers in Three Plausible NextGen Environments

    NASA Technical Reports Server (NTRS)

    Vu, Kim-Phuong L.; Strybel, Thomas Z.; Battiste, Vernol; Johnson, Walter

    2011-01-01

    In the current air traffic management (ATM) system, pilots and air traffic controllers have well-established roles and responsibilities: pilots fly aircraft and are concerned with energy management, fuel efficiency, and passenger comfort; controllers separate aircraft and are concerned with safety and management of traffic flows. Despite having different goals and obligations, both groups must be able to effectively communicate and interact with each other for the ATM system to work. This interaction will become even more challenging as traffic volume increases dramatically in the near future. To accommodate this increase, by 2025 the national air transportation system in the U.S. will go through a transformation that will modernize the ATM system and make it safer, more effective, and more efficient. This new system, NextGen, will change how pilots and controllers perform their tasks by incorporating advanced technologies and employing new procedures. It will also distribute responsibility between pilots, controllers and automation over such tasks as maintaining aircraft separation. The present chapter describes three plausible concepts of operations that allocate different ATM responsibilities to these groups. We describe how each concept changes the role of each operator and the types of decisions and actions performed by them.

  12. Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine.

    PubMed

    Takai, K; Moser, D P; Onstott, T C; Spoelstra, N; Pfiffner, S M; Dohnalkova, A; Fredrickson, J K

    2001-07-01

    A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km below land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores. Growth was observed over the temperature range 20-50 degrees C (optimum 40 degrees C; 45 min doubling time) and pH range 8.5-12.5 (optimum pH 10.0). The novel isolate, one of the most alkaliphilic micro-organisms yet described, was a strictly anaerobic chemo-organotroph capable of utilizing proteinaceous substrates such as yeast extract, peptone, tryptone and casein. Elemental sulfur, thiosulfate or fumarate, when included as accessory electron acceptors, improved growth. The G+C content of genomic DNA was 36.4 mol %. Phylogenetic analysis based on the 16S rDNA sequence indicated that the isolate is a member of cluster XI within the low G+C gram-positive bacteria, but only distantly related to previously described members. On the basis of physiological and molecular properties, the isolate represents a novel species, for which the name Alkaliphilus transvaalensis gen. nov., sp. nov. is proposed (type strain SAGM1T = JCM 10712T = ATCC 700919T). The mechanism of generation of the highly alkaline microbial habitat and the possible source of the alkaliphile are discussed. PMID:11491320

  13. Spongiivirga citrea gen. nov., sp. nov., a new marine bacterium of the family Flavobacteriaceae isolated from a marine sponge.

    PubMed

    Yoon, Jaewoo; Adachi, Kyoko; Kasai, Hiroaki; Lee, Myung-Ki

    2015-01-01

    A Gram-negative, strictly aerobic, lemon-yellow pigmented, non-motile, rod-shaped strain designated A7G-39(T) was isolated from a yellow coloured marine sponge (Tethya sp.). Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain represented a member of the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (94.1 %) to Algibacter wandonensis WS-MY22(T). The strain could be differentiated phenotypically from recognised members of the family Flavobacteriaceae. The major fatty acids of strain A7G-39(T) were identified as iso-C15:0 3-OH and summed feature 1 (iso-C15:1 H and/or C13:0 3-OH) as defined by the MIDI system. The DNA G+C content was determined to be 32.6 mol%, the major respiratory quinone was identified as menaquinone 7 (MK-7) and a polar lipid profile was present consisting of phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Spongiivirga citrea gen. nov., sp. nov. is proposed. The type strain of S. citrea is A7G-39(T) (=KCTC 32990(T) = NBRC 110022(T)). PMID:25151138

  14. Thermoactinospora rubra gen. nov., sp. nov., a thermophilic actinomycete isolated from Tengchong, Yunnan province, south-west China.

    PubMed

    Zhou, En-Min; Tang, Shu-Kun; Sjøholm, Carsten; Song, Zhao-Qi; Yu, Tian-Tian; Yang, Ling-Ling; Ming, Hong; Nie, Guo-Xing; Li, Wen-Jun

    2012-06-01

    Two novel Gram-positive, spore-forming, thermophilic actinomycetes, designated as strain YIM 77501(T) and YIM 77570, were isolated from a sandy soil sample collected at Tengchong National Volcanic Geological Park, Yunnan province, south-west China. Phylogenetic analysis based on the 16S rRNA gene sequences suggested that the two isolates fell within the family Streptosporangiaceae. The strains formed extensively branched substrate and aerial mycelia which carried masses of long, straight or irregular spore chains composed of warty ornamented spores. Cell walls of the two strains contained meso-diaminopimelic acid and glucose, galactose, mannose and ribose were detected as whole-cell sugars. The predominant menaquinones were MK-9(H(4)) and MK-9(H(6)). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, N-acetylglucosamine-containing phospholipids and phosphatidylinositol, phosphatidylinositolmannosides. The major cellular fatty acids were iso-C(16:0) and 10-methyl C(17:0). The DNA G+C content was 74-76 mol%. On the basis of the morphological and chemotaxonomic characteristics as well as the phylogenetic analysis, these strains represents a novel species of a new genus within the family Streptosporangiaceae, for which the name Thermoactinospora rubra gen. nov., sp. nov. is proposed. The type strain of T. rubra is YIM 77501(T) (=DSM 45614(T) = CCTCC AA 2011014(T)). PMID:22453518

  15. Description of Trichotokara nothriae n. gen. et sp. (Apicomplexa, Lecudinidae)--an intestinal gregarine of Nothria conchylega (Polychaeta, Onuphidae).

    PubMed

    Rueckert, Sonja; Leander, Brian S

    2010-07-01

    The trophozoites of a novel gregarine apicomplexan, Trichotokara nothriae n. gen. et sp., were isolated and characterized from the intestines of the onuphid tubeworm Nothria conchylega (Polychaeta), collected at 20 m depth from the North-eastern Pacific Coast. The trophozoites were 50-155 microm long with a mid-cell indentation that formed two prominent bulges (anterior bulge, 14-48 microm wide; posterior bulge, 15-55 microm wide). Scanning electron microscopy (SEM) demonstrated that approximately 400 densely packed, longitudinal epicytic folds (5 folds/microm) inscribe the surface of the trophozoites, and a prominently elongated mucron (14-60 microm long and 6-12 microm wide) was covered with hair-like projections (mean length, 1.97 microm; mean width, 0.2 microm at the base). Although a septum occurred at the junction between the cell proper and the mucron in most trophozoites, light microscopy (LM) demonstrated that the cell proper extended into the core of the mucron as a thin prolongation. A spherical nucleus (8-20 microm) was situated in the middle of the trophozoites, and gamonts underwent caudal syzygy. The small subunit (SSU) rDNA sequence and molecular phylogenetic position of T. nothriae was also characterized. The sequence from this species was the most divergent of all SSU rDNA sequences currently known from gregarines and formed a weakly supported clade with Lecudina polymorpha, which also possesses densely packed epicyctic folds (3-5 folds/mum) and a prominently elongated mucron. PMID:20338180

  16. Vetufebrus ovatus n. gen., n. sp. (Haemospororida: Plasmodiidae) vectored by a streblid bat fly (Diptera: Streblidae) in Dominican amber

    PubMed Central

    2011-01-01

    Background Both sexes of bat flies in the families Nycteribiidae and Streblidae (Diptera: Hippoboscoidea) reside in the hair or on the wing membranes of bats and feed on blood. Members of the Nycteribiidae transmit bat malaria globally however extant streblids have never been implemented as vectors of bat malaria. The present study shows that during the Tertiary, streblids also were vectors of bat malaria. Results A new haemospororidan, Vetufebrus ovatus, n. gen., n. sp., (Haemospororida: Plasmodiidae) is described from two oocysts attached to the midgut wall and sporozoites in salivary glands and ducts of a fossil bat fly (Diptera: Streblidae) in Dominican amber. The new genus is characterized by ovoid oocysts, short, stubby sporozoites with rounded ends and its occurrence in a fossil streblid. This is the first haemosporidian reported from a streblid bat fly and shows that representatives of the Hippoboscoidea were vectoring bat malaria in the New World by the mid-Tertiary. Conclusions This report is the first evidence of an extant or extinct streblid bat fly transmitting malaria. Discovering a mid-tertiary malarial parasite in a fossil streblid that closely resembles members of a malarial genus found in nycteribiid bat flies today shows how little we know about the vector associations of streblids. While no malaria parasites have been found in extant streblids, they probably occur and it is possible that streblids were the earliest lineage of flies that transmitted bat malaria to Chiroptera. PMID:22152687

  17. Bacterioplanes sanyensis gen. nov., sp. nov., a PHB-accumulating bacterium isolated from a pool of Spirulina platensis cultivation.

    PubMed

    Wang, Guanghua; Jia, Qikun; Li, Tao; Dai, Shikun; Wu, Huanlian; He, Hui; Fan, Jiewei; Xiang, Wenzhou; Li, Xiang

    2014-10-01

    A Gram-negative, poly-3-hydroxybutyrate-accumulating rod bacterium, strain GYP-2(T), was isolated from a pool of marine Spirulina platensis cultivation, Sanya, China. Growth was observed at 10-45 °C and pH 6-10 in the presence of 1-10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate belonged to Gammaproteobacteria and displayed 93.8-95.3 % 16S rRNA gene sequences similarities to members of the genera Thalassolituus, Oleibacter, and Oceanobacter, but house-keeping gene gyrB (encode DNA gyrase beta subunit) demonstrated that the new isolate was distantly related to Thalassolituus, Oleibacter, and Oceanobacter species (only 77-83 % gene gyrB sequences similarities).The G+C content of genomic DNA was 55 mol%. The major respiratory quinone was Q-9, while that for Oceanobacter kriegii LMG 6238(T) was Q-8. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. On the basis of its physiological, chemotaxonomic, and molecular properties, strain GYP-2(T) is suggested to represent a novel species of a new genus in Gammaproteobacteria, for which the name Bacterioplanes sanyensis gen. nov., sp. nov. is proposed. The type strain is GYP-2(T) (=CGMCC 1.12392(T)=KCTC 32220(T)). PMID:25038945

  18. Iapetonudus (N. gen.) and Iapetognathus Landing, unusual Earliest Ordovician multielement conodont taxa and their utility for biostratigraphy

    USGS Publications Warehouse

    Nicoll, R.S.; Miller, J.F.; Nowlan, G.S.; Repetski, J.E.; Ethington, Raymond L.

    1999-01-01

    The Early Ordovician (Tremadocian) multielement conodont genus Iapetognathus is one of the oldest denticulate euconodont genera known. The ramiform-ramiform apparatus structure of Iapetognathus is not similar morphologically to other Late Cambrian to Earliest Ordovician denticulate multielement taxa, such as Eodentatus or Cordyloduts, because the major denticulate process has a lateral rather than a posterior orientation as it is in the other two examples. For this reason the genus is believed to have developed from the coniform-coniform apparatus Iapetonudus ibexensis (N.gen., n.sp.) through the development of the denticulate lateral processes. The two genera have a number of morphologic features in common and appear in stratigraphic succession. Iapetognathus aengensis (Lindstro??m) is redefined as a multielement taxon using topotype material and Ig. preaengensis Landing is placed in synonymy with it. Iapetognathus sprakersi, recently described by Landing in Landing and others (1996), is recognized as a multielement species and the new multielement species, Ig. fluctivagus, Ig. jilinensis and Ig. landingi n. spp. are described herein, based on type specimens from Utah (U.S.A.), Jilin (China) and Colorado (U.S.A.) respectively. Iapetonudus and Iapetognathus are important genera in defining the level of the Cambrian-Ordovician boundary. Iapetonudus is currently recognized only from Utah, Texas and Oklahoma, but Iapetognathus is cosmopolitan in its distribution.

  19. Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov., sp. nov. and Syntrophobacter wolinii.

    PubMed

    Liu, Y; Balkwill, D L; Aldrich, H C; Drake, G R; Boone, D R

    1999-04-01

    A strain of anaerobic, syntrophic, propionate-oxidizing bacteria, strain LYPT (= OCM 661T; T = type strain), was isolated and proposed as representative of a new genus and new species, Smithella propionica gen. nov., sp. nov. The strain was enriched from an anaerobic digestor and isolated. Initial isolation was as a monoxenic propionate-degrading co-culture containing Methanospirillum hungateii JF-1T as an H2- and formate-using partner. Later, an axenic culture was obtained by using crotonate as the catabolic substrate. The previously described propionate-degrading syntrophs of the genus Syntrophobacter also grow in co-culture with methanogens such as Methanospirillum hungateii, forming acetate, CO2 and methane from propionate. However, Smithella propionica differs by producing less methane and more acetate; in addition, it forms small amounts of butyrate. Smithella propionica and Syntrophobacter wolinii grew within similar ranges of pH, temperature and salinity, but they differed significantly in substrate ranges and catabolic products. Unlike Syntrophobacter wolinii, Smithella propionica grew axenically on crotonate, although very slowly. Co-cultures of Smithella propionica grew on propionate, and grew slowly on crotonate or butyrate. Syntrophobacter wolinii and Syntrophobacter pfennigii grow on propionate plus sulfate, whereas Smithella propionica did not. Comparisons of 16S rDNA genes indicated that Smithella propionica is most closely related to Syntrophus, and is more distantly related to Syntrophobacter. PMID:10319475

  20. Desulfovirga adipica gen. nov., sp. nov., an adipate-degrading, gram-negative, sulfate-reducing bacterium.

    PubMed

    Tanaka, K; Stackebrandt, E; Tohyama, S; Eguchi, T

    2000-03-01

    A novel, mesophilic, Gram-negative bacterium was isolated from an anaerobic digestor for municipal wastewater. The bacterium degraded adipate in the presence of sulfate, sulfite, thiosulfate and elemental sulfur. (E)-2-Hexenedioate accumulated transiently in the degradation of adipate. (E)-2-Hexenedioate, (E)-3-hexenedioate, pyruvate, lactate, C1-C12 straight-chain fatty acids and C2-C10 straight-chain primary alcohols were also utilized as electron donors. 3-Phenylpropionate was oxidized to benzoate. The G + C content of the DNA was 60 mol%. 16S rDNA sequence analysis revealed that the new isolate clustered with species of the genus Syntrophobacter and Desulforhabdus amnigenus. Strain TsuAS1T resembles Desulforhabdus amnigenus DSM 10338T with respect to the ability to utilize acetate as an electron donor and the inability to utilize propionate without sulfate in co-culture with Methanospirillum hungatei DSM 864. Strains TsuAS1T and DSM 10338T form a 'non-syntrophic subcluster' within the genus Syntrophobacter. Desulfovirga adipica gen. nov., sp. nov. is proposed for the newly isolated bacterium, with strain TsuAS1T (= DSM 12016T) as the type strain. PMID:10758870

  1. Rigifila ramosa n. gen., n. sp., a filose apusozoan with a distinctive pellicle, is related to Micronuclearia.

    PubMed

    Yabuki, Akinori; Ishida, Ken-Ichiro; Cavalier-Smith, Thomas

    2013-01-01

    We report the ultrastructure, 18S and 28S rDNA sequences, and phylogenetic position of a distinctive free-living heterotrophic filose protist, Rigifila ramosa n. gen., n. sp., from a freshwater paddyfield. Rigifila lacks cilia and has a semi-rigid, radially symmetric, well-rounded, partially microtubule-supported, dorsal pellicle, and flat mitochodrial cristae. From a central aperture in a ventral depression emerges a protoplasmic stem that branches into several branching filopodia that draw bacteria to it. Electron microscopy reveals a general cell structure similar to Micronuclearia, the only non-flagellate previously known in Apusozoa; the large basal vacuole is probably an unusual giant contractile vacuole. Phylogenetic analysis of concatenated rDNA sequences groups Rigifila and Micronuclearia as sisters with maximal statistical support. However, novel morphological differences unique to Rigifila, notably a double (not single) proteinaceous layer beneath the cell membrane, and cortical microtubules, lead us to place it in a new family Rigifilidae. Our morphological and molecular analyses show that Rigifila is the closest known relative of Micronuclearia. Therefore we group Micronucleariidae and Rigifilidae as a new order Rigifilida within the existing class Hilomonadea, which now excludes planomonads. Rigifilida groups weakly with Collodictyon (Diphyllatea). We discuss the possible relationships of Rigifilida to other Apusozoa and Diphyllatea. PMID:22682062

  2. Establishment of a new hypotrichous genus, Heterotachysoma n. gen. and notes on the morphogenesis of Hemigastrostyla enigmatica (Ciliophora, Hypotrichia).

    PubMed

    Shao, Chen; Ding, Yan; Al-Rasheid, Khaled A; Al-Farraj, Saleh A; Warren, Alan; Song, Weibo

    2013-01-01

    A marine hypotrich ciliate, Heterotachysoma multinucleatum (Gong and Choi, 2007) n. comb., found in coastal waters near Qingdao, China, was investigated. Heterotachysoma multinucleatum is characterized by its dorsal ciliature arranged in Gonostomum-pattern. Additionally, a new genus, Heterotachysoma n. gen., is established which is mainly characterized by: 18-cirri pattern; flexible body; three dorsal kineties with no dorsomarginal kineties nor kinety fragmentation; one right and one left row of marginal cirri; caudal cirri absent. The genus Tachysoma is redefined, and three new combinations, T. multinucleatum, T. ovatum and T. dragescoi, are proposed. The morphogenesis of Hemigastrostyla enigmatica (Dragesco and Dragesco-Kernéis, 1986) Song and Wilbert, 1997, is also described. Compared with that of its congeners, the differences are mainly in the dorsal ciliature: (1) the dorsal kinety anlagen are formed de novo in H. enigmatica (vs. intrakinetally in H. paraenigmatica and H. elongata); (2) the dorsal kineties anlagen develop in secondary mode in H. enigmatica (vs. primary mode in H. paraenigmatica); (3) the kinetal fragment anterior to the right marginal row in both filial product is absent in both H. enigmatica and H. elongata (vs. present in H. paraenigmatica). These findings suggest that morphogenesis is not uniform among members of the genus Hemigastrostyla. PMID:22595652

  3. Reclassification of Nonomuraea flexuosa (Meyer 1989) Zhang et al. 1998 as Thermopolyspora flexuosa gen. nov., comb. nov., nom. rev.

    PubMed

    Goodfellow, Michael; Maldonado, Luis A; Quintana, Erika T

    2005-09-01

    A polyphasic study was undertaken to clarify the taxonomic position of Nonomuraea flexuosa DSM 41386(T). The distinct 16S rRNA gene sequence phyletic branch formed by this strain was equated with nine related monophyletic clades composed of representatives of the genera classified in the family Streptosporangiaceae. The organism produced a PCR product characteristic of this taxon when examined using a set of oligonucleotide primers specific for members of the family Streptosporangiaceae. Strain DSM 41386(T) could also be distinguished from representatives of the nine genera assigned to this family using a combination of chemotaxonomic, morphological and physiological properties. It is evident from the genotypic and phenotypic data that strain DSM 41386(T) is misclassified in the genus Nonomuraea and merits recognition as a monospecific genus within the family Streptosporangiaceae. It is proposed that the name Thermopolyspora flexuosa gen. nov., comb. nov., nom. rev. be used for this purpose, with the type strain DSM 41386(T) (=NRRL B-24348(T)). PMID:16166698

  4. The smallest Cyrtoscydmini of Australia: revision of Microscydmus Saulcy & Croissandeau and Penicillidmus gen. n.(Coleoptera, Staphylinidae, Scydmaeninae).

    PubMed

    Ja?oszy?ski, Pawe?

    2014-01-01

    The Australian members of Microscydmus are revised, and a new subgenus Scydmomicrus subgen. n. is established to accommodate seven species: M. (Sc.) australiensis Franz (type species of Scydmomicrus), M. (Sc.) nasicornis Franz, M. (Sc.) capitiseboraci sp. n., M. (Sc.) queenslandicus sp. n., M. (Sc.) styxianus sp. n., M. (Sc.) edithensis sp. n., and M. (Sc.) tooloomensis sp. n. A new Microscydmus-like genus, Penicillidmus gen. n., is described to include Penicillidmus masseyensis sp. n. (type species of Penicillidmus) and P. unicolor sp. n. Species of Microscydmus and Penicillidmus are distributed along the eastern coast of Australia, from the northern Cape York to northeastern New South Wales, and females of an undescribed Microscydmus are recorded from southern New South Wales. The revised taxa comprise the smallest Australian Cyrtoscydmini, with body lengths of only 0.50-0.65 mm (Microscydmus) and 0.83-0.86 mm (Penicillidmus). For comparative purposes, morphological details of the type species of Microscydmus, M. nanus, are described, and structures of the new subgenus and new genus are illustrated. Variations of character states within Microscydmus found among Australian species are discussed. PMID:24871402

  5. Moorea producens gen. nov., sp. nov. and Moorea bouillonii comb. nov., tropical marine cyanobacteria rich in bioactive secondary metabolites.

    PubMed

    Engene, Niclas; Rottacker, Erin C; Kaštovský, Jan; Byrum, Tara; Choi, Hyukjae; Ellisman, Mark H; Komárek, Ji?í; Gerwick, William H

    2012-05-01

    The filamentous cyanobacterial genus Moorea gen. nov., described here under the provisions of the International Code of Botanical Nomenclature, is a cosmopolitan pan-tropical group abundant in the marine benthos. Members of the genus Moorea are photosynthetic (containing phycocyanin, phycoerythrin, allophycocyanin and chlorophyll a), but non-diazotrophic (lack heterocysts and nitrogenase reductase genes). The cells (discoid and 25-80 µm wide) are arranged in long filaments (<10 cm in length) and often form extensive mats or blooms in shallow water. The cells are surrounded by thick polysaccharide sheaths covered by a rich diversity of heterotrophic micro-organisms. A distinctive character of this genus is its extraordinarily rich production of bioactive secondary metabolites. This is matched by genomes rich in polyketide synthase and non-ribosomal peptide synthetase biosynthetic genes which are dedicated to secondary metabolism. The encoded natural products are sometimes responsible for harmful algae blooms and, due to morphological resemblance to the genus Lyngbya, this group has often been incorrectly cited in the literature. We here describe two species of the genus Moorea: Moorea producens sp. nov. (type species of the genus) with 3L(T) as the nomenclature type, and Moorea bouillonii comb. nov. with PNG5-198(R) as the nomenclature type. PMID:21724952

  6. Homoserinimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea.

    PubMed

    Kim, Soo-Jin; Jang, Yun-Hee; Hamada, Moriyuki; Tamura, Tomohiko; Ahn, Jae-Hyung; Weon, Hang-Yeon; Suzuki, Ken-Ichiro; Kwon, Soon-Wo

    2012-08-01

    A bacterial strain isolated from an air sample, strain 5317J-19(T), was characterized. The isolate was an aerobic, motile, Gram-positive rod. The organism was able to grow between 4 and 35°C and between pH 6 and 9. The predominant fatty acids were anteiso-C(15:0) and iso-C(16:0). The major respiratory menaquinones were MK-12 and MK-11, and the minor ones were MK13, MK-10, and MK-9. Genomic DNA G+C content was 66 mol%. The diagnostic diamino acid of the peptidoglycan is presumably D-Orn. The peptidoglycan is supposed to be B2? type. The 16S rRNA gene sequence analysis indicated that this isolate belongs to the family Microbacteriaceae and had the highest sequence similarities with Salinibacterium xinjiangense 0543(T) (97.6%), Salinibacterium amurskyense KMM 3673(T) (97.2%), and Leifsonia bigeumensis MSL-27(T) (97.2%). Phylogenetic analysis and phenotypic characteristics support the proposal of a new genus and a novel species, with the name Homoserinimonas aerilata gen. nov., sp. nov. The type strain of Homoserinimonas aerilata is 5317J-19(T) (=KACC 15522(T) =NBRC 108729(T)). PMID:22923118

  7. The Ultramicrobacterium “Elusimicrobium minutum” gen. nov., sp. nov., the First Cultivated Representative of the Termite Group 1 Phylum? †

    PubMed Central

    Geissinger, Oliver; Herlemann, Daniel P. R.; Mörschel, Erhard; Maier, Uwe G.; Brune, Andreas

    2009-01-01

    Insect intestinal tracts harbor several novel, deep-rooting clades of as-yet-uncultivated bacteria whose biology is typically completely unknown. Here, we report the isolation of the first representative of the termite group 1 (TG1) phylum from sterile-filtered gut homogenates of a humivorous scarab beetle larva. Strain Pei191T is a mesophilic, obligately anaerobic ultramicrobacterium with a gram-negative cell envelope. Cells are typically rod shaped, but cultures are pleomorphic in all growth phases (0.3 to 2.5 ?m long and 0.17 to 0.3 ?m wide). The isolate grows heterotrophically on sugars and ferments d-galactose, d-glucose, d-fructose, d-glucosamine, and N-acetyl-d-glucosamine to acetate, ethanol, hydrogen, and alanine as major products but only if amino acids are present in the medium. PCR-based screening and comparative 16S rRNA gene sequence analysis revealed that strain Pei191T belongs to the “intestinal cluster,” a lineage of hitherto uncultivated bacteria present in arthropod and mammalian gut systems. It is only distantly related to the previously described so-called “endomicrobia” lineage, which comprises mainly uncultivated endosymbionts of termite gut flagellates. We propose the name “Elusimicrobium minutum” gen. nov., sp. nov. (type strain, Pei191T = ATCC BAA-1559T = JCM 14958T) for the first isolate of this deep-branching lineage and the name “Elusimicrobia” phyl. nov. for the former TG1 phylum. PMID:19270135

  8. Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of 'Corynebacterium aquaticum' Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov.

    PubMed

    Evtushenko, L I; Dorofeeva, L V; Subbotin, S A; Cole, J R; Tiedje, J M

    2000-01-01

    The new genus Leifsonia gen. nov. with two new species, Leifsonia poae sp. nov. (type strain VKM Ac-1401T) and Leifsonia aquatica (ex Leifson 1962) nom. rev., comb. nov. (the type species, with VKM Ac-1400T = DSM 20146T = JCM 1368T as type strain), is proposed to accommodate bacteria found in Poa annua root gall, induced by the nematode Subanguina radicicola, and 'Corynebacterium aquaticum' Leifson 1962. Further, it is proposed to reclassify Clavibacter xyli Davis et al. 1984 with two subspecies in the new genus as Leifsonia xyli (Davis et al. 1984) comb. nov., Leifsonia xyli subsp. xyli (Davis et al. 1984) comb. nov. and Leifsonia xyli subsp. cynodontis (Davis et al. 1984) comb. nov. Members of the proposed genus are characterized by coryneform morphology, peptidoglycans based upon 2,4-diaminobutyric acid, the major menaquinone MK-11, phosphatidylglycerol and diphosphatidylglycerol as principal phospholipids, the high content of anteiso- and iso-branched saturated fatty acids, and a DNA G+C base composition of 66-73 mol%. They form a distinct phylogenetic branch attached to the line of descent of Agromyces spp. The new and reclassified species of the new genus clearly differ from each other phylogenetically and phenetically and can be recognized by their morphologies, the cell wall sugar composition, the requirement of complex media for growth, and numerous physiological characteristics, including the oxidase reaction. PMID:10826825

  9. Tomitella biformata gen. nov., sp. nov., a new member of the suborder Corynebacterineae isolated from a permafrost ice wedge.

    PubMed

    Katayama, Taiki; Kato, Tomoko; Tanaka, Michiko; Douglas, Thomas A; Brouchkov, Anatoli; Abe, Ayumi; Sone, Teruo; Fukuda, Masami; Asano, Kozo

    2010-12-01

    Gram-reaction-positive, aerobic, non-spore-forming, irregular rod-shaped bacteria, designated AHU1821(T) and AHU1820, were isolated from an ice wedge in the Fox permafrost tunnel, Alaska. The strains were psychrophilic, growing at -5 to 27°C. Phylogenetic analysis of the 16S rRNA and gyrB gene sequences indicated that the ice-wedge isolates formed a clade distinct from other mycolic-acid-containing bacteria within the suborder Corynebacterineae. The cell wall of strains AHU1821(T) and AHU1820 contained meso-diaminopimelic acid, arabinose and galactose, indicating chemotype IV. The muramic acids in the peptidoglycan were glycolated. The predominant menaquinone was MK-9(H(2)). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unidentified glycolipid. The major fatty acids were hexadecenoic acid (C(16?:?1)), hexadecanoic acid (C(16?:?0)), octadecenoic acid (C(18?:?1)) and tetradecanoic acid (C(14?:?0)). Tuberculostearic acid was present in relatively small amounts (1?%). Strains AHU1821(T) and AHU1820 contained mycolic acids with 42-52 carbons. The DNA G+C content of the two strains was 69.3-71.6 mol% (T(m)). 16S rRNA, rpoB and recA gene sequences were identical between strains AHU1821(T) and AHU1820 and those of the gyrB gene showed 99.9?% similarity. Based on phylogenetic and phenotypic evidence, strains AHU1821(T) and AHU1820 represent a single novel species of a novel genus, for which the name Tomitella biformata gen. nov., sp. nov. is proposed. The type strain of Tomitella biformata is AHU1821(T) (=DSM 45403(T) =NBRC 106253(T)). PMID:20081023

  10. GenTAC Registry Report: Gender Differences Among Individuals with Genetically-Triggered Thoracic Aortic Aneurysm and Dissection

    PubMed Central

    Holmes, Kathryn W.; Maslen, Cheryl L.; Kindem, Mark; Kroner, Barbara L.; Song, Howard K.; Ravekes, William; Dietz, H.C.; Weinsaft, Jonathan W.; Roman, Mary J.; Devereux, Richard B.; Pyeritz, Reed E.; Bavaria, Joseph; Milewski, Karianna; Milewicz, Dianna; LeMaire, Scott A.; Hendershot, Tabitha; Eagle, Kim A.; Tolunay, H. Eser; Desvigne-Nickens, Patrice; Silberbach, Michael

    2013-01-01

    Previous data suggest women are at increased risk of death from aortic dissection. Therefore, we analyzed data from the GenTAC registry, the NIH-sponsored program that collects information about individuals with genetically-triggered thoracic aortic aneurysms and cardiovascular conditions. We performed cross-sectional analyses in adults with Marfan syndrome (MFS), familial thoracic aortic aneurysm or dissection (FTAAD), bicuspid aortic valve (BAV) with thoracic aortic aneurysm or dissection, and subjects under 50 years of age with thoracic aortic aneurysm or dissection (TAAD<50y). Women comprised 32% of 1449 subjects and were 21% of subjects with BAV, 34% with FTAAD, 22% with TAAD <50y, and 47% with MFS. Thoracic aortic dissections occurred with equal gender frequency yet women with BAV had more extensive dissections. Aortic size was smaller in women but was similar after controlling for BSA. Age at operation for aortic valve dysfunction, aneurysm or dissection did not differ by gender. Multivariate analysis (adjusting for age, BSA, hypertension, study site, diabetes, and subgroup diagnoses) showed that women had fewer total aortic surgeries (OR= 0.65, p < 0.01) and were less likely to receive angiotensin converting enzyme inhibitors (ACEi) (OR=0.68, p < 0.05). As in BAV, other genetically-triggered aortic diseases such as FTAAD and TAAD<50 are more common in males. In women, decreased prevalence of aortic operations and less treatment with ACEi may be due to their smaller absolute aortic diameters. Longitudinal studies are needed to determine if women are at higher risk for adverse events. PMID:23444191

  11. A New Troodontid Theropod, Talos sampsoni gen. et sp. nov., from the Upper Cretaceous Western Interior Basin of North America

    PubMed Central

    Zanno, Lindsay E.; Varricchio, David J.; O'Connor, Patrick M.; Titus, Alan L.; Knell, Michael J.

    2011-01-01

    Background Troodontids are a predominantly small-bodied group of feathered theropod dinosaurs notable for their close evolutionary relationship with Avialae. Despite a diverse Asian representation with remarkable growth in recent years, the North American record of the clade remains poor, with only one controversial species—Troodon formosus—presently known from substantial skeletal remains. Methodology/Principal Findings Here we report a gracile new troodontid theropod—Talos sampsoni gen. et sp. nov.—from the Upper Cretaceous Kaiparowits Formation, Utah, USA, representing one of the most complete troodontid skeletons described from North America to date. Histological assessment of the holotype specimen indicates that the adult body size of Talos was notably smaller than that of the contemporary genus Troodon. Phylogenetic analysis recovers Talos as a member of a derived, latest Cretaceous subclade, minimally containing Troodon, Saurornithoides, and Zanabazar. MicroCT scans reveal extreme pathological remodeling on pedal phalanx II-1 of the holotype specimen likely resulting from physical trauma and subsequent infectious processes. Conclusion/Significance Talos sampsoni adds to the singularity of the Kaiparowits Formation dinosaur fauna, which is represented by at least 10 previously unrecognized species including the recently named ceratopsids Utahceratops and Kosmoceratops, the hadrosaurine Gryposaurus monumentensis, the tyrannosaurid Teratophoneus, and the oviraptorosaurian Hagryphus. The presence of a distinct troodontid taxon in the Kaiparowits Formation supports the hypothesis that late Campanian dinosaurs of the Western Interior Basin exhibited restricted geographic ranges and suggests that the taxonomic diversity of Late Cretaceous troodontids from North America is currently underestimated. An apparent traumatic injury to the foot of Talos with evidence of subsequent healing sheds new light on the paleobiology of deinonychosaurians by bolstering functional interpretations of prey grappling and/or intraspecific combat for the second pedal digit, and supporting trackway evidence indicating a minimal role in weight bearing. PMID:21949721

  12. Desulfovirgula thermocuniculi gen. nov., sp. nov., a thermophilic sulfate-reducer isolated from a geothermal underground mine in Japan.

    PubMed

    Kaksonen, Anna H; Spring, Stefan; Schumann, Peter; Kroppenstedt, Reiner M; Puhakka, Jaakko A

    2007-01-01

    A thermophilic, Gram-positive, endospore-forming, sulfate-reducing bacterial strain, designated RL80JIV(T), was isolated from a geothermally active underground mine in Japan. Cells were rod-shaped and motile. The temperature and pH ranges for growth were 61-80 degrees C (optimum at 69-72 degrees C) and pH 6.4-7.9 (optimum at pH 6.8-7.3), and the strain tolerated up to 0.5 % NaCl. Strain RL80JIV(T) utilized sulfate, sulfite, thiosulfate and elemental sulfur as electron acceptors. Electron donors utilized were H(2) in the presence of CO(2), and carboxylic acids. Fermentative growth occurred on lactate and pyruvate. The cell wall contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was menaquinone MK-7. Major whole-cell fatty acids were iso-C(15 : 0), iso-C(17 : 0) and C(16 : 0). Strain RL80JIV(T) was found to be affiliated with the thiosulfate-reducer Thermanaeromonas toyohensis DSM 14490(T) (90.9 % 16S rRNA gene sequence similarity) and with the sulfate-reducer Desulfotomaculum thermocisternum DSM 10259(T) (90.0 % similarity). Strain RL80JIV(T) is therefore considered to represent a novel species of a new genus, for which the name Desulfovirgula thermocuniculi gen. nov., sp. nov. is proposed. The type strain of Desulfovirgula thermocuniculi is RL80JIV(T) (=DSM 16036(T)=JCM 13928(T)). PMID:17220449

  13. GenTAC registry report: gender differences among individuals with genetically triggered thoracic aortic aneurysm and dissection.

    PubMed

    Holmes, Kathryn W; Maslen, Cheryl L; Kindem, Mark; Kroner, Barbara L; Song, Howard K; Ravekes, William; Dietz, H C; Weinsaft, Jonathan W; Roman, Mary J; Devereux, Richard B; Pyeritz, Reed E; Bavaria, Joseph; Milewski, Karianna; Milewicz, Dianna; LeMaire, Scott A; Hendershot, Tabitha; Eagle, Kim A; Tolunay, H Eser; Desvigne-Nickens, Patrice; Silberbach, Michael

    2013-04-01

    Previous data suggest women are at increased risk of death from aortic dissection. Therefore, we analyzed data from the GenTAC registry, the NIH-sponsored program that collects information about individuals with genetically triggered thoracic aortic aneurysms and cardiovascular conditions. We performed cross-sectional analyses in adults with Marfan syndrome (MFS), familial thoracic aortic aneurysm or dissection (FTAAD), bicuspid aortic valve (BAV) with thoracic aortic aneurysm or dissection, and subjects under 50 years of age with thoracic aortic aneurysm or dissection (TAAD <50 years). Women comprised 32% of 1,449 subjects and were 21% of subjects with BAV, 34% with FTAAD, 22% with TAAD <50 years, and 47% with MFS. Thoracic aortic dissections occurred with equal gender frequency yet women with BAV had more extensive dissections. Aortic size was smaller in women but was similar after controlling for BSA. Age at operation for aortic valve dysfunction, aneurysm or dissection did not differ by gender. Multivariate analysis (adjusting for age, BSA, hypertension, study site, diabetes, and subgroup diagnoses) showed that women had fewer total aortic surgeries (OR = 0.65, P < 0.01) and were less likely to receive angiotensin converting enzyme inhibitors (ACEi; OR = 0.68, P < 0.05). As in BAV, other genetically triggered aortic diseases such as FTAAD and TAAD <50 are more common in males. In women, decreased prevalence of aortic operations and less treatment with ACEi may be due to their smaller absolute aortic diameters. Longitudinal studies are needed to determine if women are at higher risk for adverse events. PMID:23444191

  14. Jeotgalicoccus halotolerans gen. nov., sp. nov. and Jeotgalicoccus psychrophilus sp. nov., isolated from the traditional Korean fermented seafood jeotgal.

    PubMed

    Yoon, Jung-Hoon; Lee, Keun-Chul; Weiss, Norbert; Kang, Kook Hee; Park, Yong-Ha

    2003-03-01

    Two Gram-positive, non-motile, non-spore-forming, halotolerant and moderately halophilic cocci (strains YKJ-101T and YKJ-115T) were isolated from the traditional Korean fermented seafood jeotgal, and were investigated using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rDNA sequences showed that strains YKJ-101T and YKJ-115T are most closely related to the cluster comprising two Salinicoccus species. The peptidoglycan type of the strains is A3alpha, based on L-Lys-Gly(3-4)-L-Ala(Gly), and the predominant menaquinone is MK-7. Strains YKJ-101T and YKJ-115T have cellular fatty acid profiles containing major amounts of saturated, unsaturated and branched fatty acids; the major fatty acids are anteiso-C15 : 0 and iso-C15 : 0. The cellular polar lipids are phosphatidylglycerol, diphosphatidylglycerol and unidentified phospholipids. Strains YKJ-101T and YKJ-115T have identical DNA G + C contents of 42 mol%. The 16S rDNA similarity between strains YKJ-101T and YKJ-115T is 98% and the mean level of DNA-DNA relatedness between the two strains is 13.4%. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, it is proposed that strains YKJ-101T and YKJ-115T should be placed in a new genus, Jeotgalicoccus gen. nov., as two distinct new species, for which the names Jeotgalicoccus halotolerans sp. nov. and Jeotgalicoccus psychrophilus sp. nov. are proposed. The type strains are YKJ-101T (=KCCM 41448T =JCM 11198T) and YKJ-115T (=KCCM 41449T =JCM 11199T), respectively. PMID:12710632

  15. Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite.

    PubMed

    Zhang, De-Chao; Redzic, Mersiha; Schinner, Franz; Margesin, Rosa

    2011-09-01

    Strains Cr9-30(T) and Cr9-12 were isolated from alpine glacier cryoconite. Both strains were Gram-negative-staining, non-motile, rod-shaped and psychrophilic, showing good growth over the temperature range 1-20 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that the two strains formed a distinct branch within the family Oxalobacteraceae and were most closely related to members of the genus Collimonas. The 16S rRNA gene sequence similarity between strains Cr9-30(T) and Cr9-12 was 99.0?%. The two strains showed highest 16S rRNA gene sequence pairwise similarity with Collimonas pratensis LMG 23965(T) (96.6 and 96.1?% for strains Cr9-30(T) and Cr9-12, respectively), Collimonas arenae LMG 23964(T) (96.5 and 96.3?%, respectively) and Collimonas fungivorans LMG 21973(T) (96.4 and 96.2?%, respectively). The predominant cellular fatty acids were summed feature 3 (C??:??7c and/or iso-C??:? 2-OH), C??:? and C??:??7c. The DNA G+C content of strain Cr9-30(T) was 51.0 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strains Cr9-30(T) and Cr9-12 represent a novel species in a new genus of the family Oxalobacteraceae, for which the name Glaciimonas immobilis gen. nov., sp. nov. is proposed. The type strain of Glaciimonas immobilis is Cr9-30(T) (?=?DSM 23240(T)?=?LMG 25547(T)). PMID:20935085

  16. Alpinimonas psychrophila gen. nov., sp. nov., an actinobacterium of the family Microbacteriaceae isolated from alpine glacier cryoconite.

    PubMed

    Schumann, Peter; Zhang, De-Chao; Redzic, Mersiha; Margesin, Rosa

    2012-11-01

    A Gram-type positive, Gram-reaction variable, non-motile, psychrophilic actinobacterium, designated Cr8-25(T), was isolated from alpine glacier cryoconite and was able to grow well over a temperature range of 1-15 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Cr8-25(T) belonged to the family Microbacteriaceae and showed highest 16S rRNA gene sequence similarity with Klugiella xanthotipulae 44C3(T) (97.0%). However, strain Cr8-25(T) could be differentiated from the type strain of K. xanthotipulae on the level of genomospecies by a DNA-DNA relatedness value of only 37.2%. Strain Cr8-25(T) contained a cell-wall peptidoglycan that was cross-linked according to the B-type, which is based on 2,4-diaminobutyric acid. The cell wall contained the sugars galactose, fucose and rhamnose. The predominant cellular fatty acids of strain Cr8-25(T) were C(15:0) anteiso (64.6%) and iso-C(16:0) (22.5%) and the major menaquinones were MK-11 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids. The G+C content of the genomic DNA was 58.8 mol%. On the basis of the phenotypic characteristics, phylogenetic and chemotaxonomic analyses and DNA-DNA relatedness data, strain Cr8-25(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Alpinimonas psychrophila gen. nov., sp. nov. is proposed. The type strain is Cr8-25(T) (=DSM 23737(T)=LMG 26215(T)). PMID:22228665

  17. Pricia antarctica gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from Antarctic intertidal sediment.

    PubMed

    Yu, Yong; Li, Hui-Rong; Zeng, Yin-Xin; Sun, Kun; Chen, Bo

    2012-09-01

    A yellow-coloured, rod-shaped, Gram-reaction- and Gram-staining-negative, non-motile and aerobic bacterium, designated strain ZS1-8(T), was isolated from a sample of sandy intertidal sediment collected from the Antarctic coast. Flexirubin-type pigments were absent. In phylogenetic analyses based on 16S rRNA gene sequences, strain ZS1-8(T) formed a distinct phyletic line and the results indicated that the novel strain should be placed in a new genus within the family Flavobacteriaceae. In pairwise comparisons between strain ZS1-8(T) and recognized species, the levels of 16S rRNA gene sequence similarity were all <93.3 %. The strain required Ca(2+) and K(+) ions as well as NaCl for growth. Optimal growth was observed at pH 7.5-8.0, 17-19 °C and with 2-3 % (w/v) NaCl. The major fatty acids were iso-C(15 : 1) G, iso-C(15 : 0), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)?7c), an unknown acid with an equivalent chain-length of 13.565 and iso-C(17 : 0) 3-OH. The major respiratory quinone was MK-6. The predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 43.9 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain ZS1-8(T) represents a novel species in a new genus in the family Flavobacteriaceae for which the name Pricia antarctica gen. nov., sp. nov. is proposed. The type strain of the type species is ZS1-8(T) (= JCM 17291(T) = DSM 23421(T)). PMID:22081722

  18. Roseicitreum antarcticum gen. nov., sp. nov., an aerobic bacteriochlorophyll a-containing alphaproteobacterium isolated from Antarctic sandy intertidal sediment.

    PubMed

    Yu, Yong; Yan, Shu-Lin; Li, Hui-Rong; Zhang, Xiao-Hua

    2011-09-01

    A novel Gram-negative, non-motile bacterium, designated strain ZS2-28(T), was isolated from sandy intertidal sediment samples collected from the coastal regions of the Chinese Antarctic Zhongshan Station on the Larsemann Hills, Princess Elizabeth Land, East Antarctica. Strain ZS2-28(T) was obligately heterotrophic, strictly aerobic, psychrotolerant (growth occurred at 0-33 °C) and moderately halophilic (optimal growth in 7-8?% NaCl). A single major peak at 872-874 nm in the infrared absorption spectrum indicated the presence of bacteriochlorophyll a. Poly-?-hydroxybutyrate accumulation and slime production were also detected. The predominant cellular fatty acid was C??:??7c, with C??:? 3-OH, C??:?, C??:? cyclo, C??:??8c cyclo and summed feature 3 (C??:??7c and/or iso-C??:? 2-OH) present in smaller amounts. The respiratory quinone was Q-10. The main polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified aminolipid. The G+C content of the genomic DNA was 63.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZS2-28(T) formed a distinct evolutionary lineage within the clade containing members of the genera Roseibaca, Roseinatronobacter and Rhodobaca of the class Alphaproteobacteria. On the basis of its phylogenetic position, as well as its phenotypic and chemotaxonomic characteristics, strain ZS2-28(T) represents a novel species of a novel genus, for which the name Roseicitreum antarcticum gen. nov., sp. nov. is proposed. The type strain is ZS2-28(T) (?=?CGMCC 1.8894(T) ?=?LMG 24863(T)). PMID:20889763

  19. Tabrizicola aquatica gen. nov. sp. nov., a novel alphaproteobacterium isolated from Qurugöl Lake nearby Tabriz city, Iran.

    PubMed

    Tarhriz, Vahideh; Thiel, Vera; Nematzadeh, Ghorbanali; Hejazi, Mohammad Amin; Imhoff, Johannes F; Hejazi, Mohammad Saeid

    2013-12-01

    A novel Gram-negative, aerobic, non-motile and rod-shaped bacterium was isolated from Qurugöl Lake near Tabriz city. The bacterium grew chemoorganolheterotrophically and chemolithoautotrophically. However, photo-organoheterotrophic, photo-lithoautotrophic and fermentative growth could not be demonstrated. The presence of photosynthesis genes pufL and pufM was not shown and photosynthesis pigments were not formed. Strain RCRI19(T) grew without NaCl and tolerated up to 3 % NaCl. Growth occurred at pH 6-9 (optimum, pH 7) and 15-55 °C (optimum 40-45 °C). Vitamins were not required for growth. The major fatty acids are C18:1 ?7C, 11-methyl C18:1 ?7C, C18:0 3-OH. The predominant respiratory quinone is ubiquinone Q-10. The G+C content of genomic DNA is 65.9 mol%. Analysis of 16S rRNA sequences showed that strain RCRI19(T) has the highest similarities with uncultured environmental sequences followed by members of the genera Rhodobacter (?95.75 %), Haematobacter (?95.53 %), Gemmobacter (?95.17 %) and Falsirhodobacter (94.60 %) in the family Rhodobacteraceae. DNA-DNA relatedness between strain RCRI19(T) and the closest phylogenetically related strain, Rhodobacter blasticus LMG 4305(T), was 20 %. Based on its phenotypic and chemotaxonomic characteristics and considering that it does not form photosynthetic pigments and is unable to grow phototrophically, it is concluded that strain RCRI19(T) cannot be included into the genus Rhodobacter and any of the other related genera. Therefore, we propose to place the new bacterium into a new genus and species for which the name Tabrizicola aquatica gen. nov. and sp. nov. is proposed. The type strain is RCRI19(T) (=BCCM/LMG 25773(T )= JCM 17277(T )= KCTC 23724(T)). PMID:24158532

  20. Salinarubrum litoreum gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from Chinese marine solar salterns.

    PubMed

    Cui, Heng-Lin; Qiu, Xing-Xing

    2014-01-01

    Three halophilic archaeal strains, XD46(T), YJ-63-S1 and ZS-1-H, were isolated from three Chinese marine solar salterns. All were observed to have pleomorphic cells that lysed in distilled water, stained Gram-negative and formed red-pigmented colonies. They were found to grow optimally at 37 °C, at pH 7.0 and in the presence of 2.6 M NaCl and 0.05 M Mg(2+). The major polar lipids were identified as those typical for members of the Halobacteriaceae but also included major glycolipids chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1), mannosyl glucosyl diether (DGD-1) and two unidentified ones. The 16S rRNA gene sequences of the three strains were 99.8-100 % identical, showing most similarity to sequences of members of the family Halobacteriaceae, and clustering together as a distinct clade in phylogenetic tree reconstructions. The rpoB' gene similarities between the three strains were 98.7-100 % and lower to the sequences of other halobacteria. Their DNA G+C contents were determined to be 65.1-65.5 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains XD46(T) (=CGMCC 1.12237(T) = JCM 18649(T)), YJ-63-S1 (=CGMCC 1.12574) and ZS-1-H (=CGMCC 1.12544) represent a novel species in a new genus within the family Halobacteriaceae, for which the name Salinarubrum litoreum gen. nov., sp. nov. is proposed. PMID:24158535

  1. Aliicoccus persicus gen. nov., sp. nov., a halophilic member of the Firmicutes isolated from a hypersaline lake.

    PubMed

    Amoozegar, Mohammad Ali; Bagheri, Maryam; Makhdoumi-Kakhki, Ali; Didari, Maryam; Schumann, Peter; Nikou, Mahdi Moshtaghi; Sánchez-Porro, Cristina; Ventosa, Antonio

    2014-06-01

    A novel Gram-staining-positive, moderately halophilic bacterium, designated strain A76(T), was isolated from a brine sample of the hypersaline lake Aran-Bidgol in Iran. Cells were strictly aerobic, coccus-shaped, non-motile, non-sporulating, and catalase- and oxidase-positive. Strain A76(T) grew between pH 7.0 and 10.0 (optimal growth at pH 8.0), between 20 and 45 °C (optimal growth at 35 °C) and at salinities of 0.5 to 12.5% (w/v) NaCl (optimal growth at 7.5%, w/v, NaCl). On the basis of 16S rRNA gene sequence analysis, strain A76(T) was shown to belong to the phylum Firmicutes with sequence similarities of 94.1, 93.1 and 91.1%, to the type species of the genera Jeotgalicoccus, Salinicoccus and Nosocomiicoccus, respectively. The DNA G+C content of this new isolate was 38.8 mol%. The major cellular fatty acids of strain A76(T) were anteiso-C(15?:?0) and iso-C(15?:?0), and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, a glycolipid, an unknown lipid and two unknown phospholipids. The isoprenoid quinones were MK-6 (94%), MK-5 (3%) and MK-7 (3%). The amino acid constituents of the cell wall were Lys, Asp, Gly, Glu and Ala. The physiological, biochemical and phylogenetic differences between strain A76(T) and type strains of taxa with validly published names suggest that this strain represents a novel species in a novel genus within the family Staphylococcaceae, for which the name Aliicoccus persicus gen. nov., sp. nov. is proposed. The type strain of Aliicoccus persicus is strain A76(T) (?=?CECT 8508(T)?=?DSM 28306(T)?=?IBRC-M 10081(T)). PMID:24599898

  2. Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a new anaerobic, slightly halophilic, thiosulfate-reducing bacterium from corroding offshore oil wells.

    PubMed

    Magot, M; Ravot, G; Campaignolle, X; Ollivier, B; Patel, B K; Fardeau, M L; Thomas, P; Crolet, J L; Garcia, J L

    1997-07-01

    A strictly anaerobic thiosulfate-reducing bacterium was isolated from a corroding offshore oil well in Congo and was designated strain SEBR 4207T. Pure culture of the strain induced a very active pitting corrosion of mild steel, with penetration rates of up to 4 mm per year. This constitutes the first experimental evidence of the involvement of thiosulfate reduction in microbial corrosion of steel. Strain SEBR 4207T cells were vibrios (3 to 5 by 1 microns), stained gram negative, and possessed lateral flagella. Spores were not detected. Optimum growth occurred in the presence of 3% NaCl at pH 7.0 and 42 degrees C. Strain SEBR 4207T utilized peptides and amino acids, but not sugars or fatty acids. It fermented serine, histidine, and Casamino Acids, whereas arginine, glutamate, leucine, isoleucine, alanine, valine, methionine, and asparagine were only used in the presence of thiosulfate. Peptides were fermented to acetate, isobutyrate, isovalerate, 2-methylbutyrate, H2, and CO2. The addition of either thiosulfate or sulfur but not sulfate increased peptide utilization, growth rate, and biomass; during growth, H2S was produced and a concomitant decrease in H2 was observed. The addition of either thiosulfate or sulfur also reversed H2 inhibition. 16S rRNA sequence analysis indicates that strain SEBR 4207T is distantly related to members of the genus Thermoanaerobacter (83% similarity). Because the phenotypic and phylogenetic characteristics cannot be assigned to any described genus, strain SEBR 4207T is designated as a new species of a new genus, Dethiosulfovibrio peptidovorans gen. nov., sp. nov. Strain SEBR 4207T has been deposited in the Deutsche Sammlung von Mikroorganismen und zellkulturen GmbH (= DSM 11002). PMID:9226912

  3. Alkanindiges illinoisensis gen. nov., sp. nov., an obligately hydrocarbonoclastic, aerobic squalane-degrading bacterium isolated from oilfield soils.

    PubMed

    Bogan, Bill W; Sullivan, Wendy R; Kayser, Kevin J; Derr, K D; Aldrich, Henry C; Paterek, J Robert

    2003-09-01

    An alkane-degrading bacterium, designated GTI MVAB Hex1(T), was isolated from chronically crude oil-contaminated soil from an oilfield in southern Illinois. The isolate grew very weakly or not at all in minimal or rich media without hydrocarbons. Straight-chain aliphatic hydrocarbons, such as hexadecane and heptadecane, greatly stimulated growth; shorter-chain (gen. nov., sp. nov. is proposed, which is most closely related (approx. 94 % sequence similarity) to Acinetobacter junii. PMID:13130023

  4. Cobbania corrugata gen. et comb. nov. (Araceae): a floating aquatic monocot from the Upper Cretaceous of western North America.

    PubMed

    Stockey, Ruth A; Rothwell, Gar W; Johnson, Kirk R

    2007-04-01

    The fossil record of aquatic flowering plants broadens our understanding of their former diversity and origins from terrestrial ancestors. This paper describes a floating aquatic monocot from 71 whole plants and several isolated leaf fragments from Upper Cretaceous oxbow lake sediments in the Dinosaur Park Formation, Alberta, Canada. The new material is represented by rosettes of leaves and roots attached to short stems that are interconnected by stolons and corresponds to the fossil aroid originally described as Pistia corrugata Lesquereux. Up to six plants have been found interconnected on a single slab suggesting that these plants grew in extensive floating mats covering lakes and calm stretches of rivers. Stems have up to six leaves and large numbers of branched aquatic roots. The leaf is trumpet-shaped with an elongate clasping petiole, large aerenchymatous base, and a nearly circular blade rim. Leaf bases are often filled with sediment giving the leaf the appearance of having a basal pouch. Petioles have 6-9 veins that divide into an upper and lower set, and veins converge at an apical notch. A submarginal collective vein and at least two marginal veins with branching veins form the leaf rim. A series of dichotomizing and anastomosing veins characterize the adaxial leaf surface. Tertiary and quaternary veins form polygonal areolae. Leaf surfaces are covered in trichomes that, like those in Pistia stratiotes, probably aided in buoyancy. A reconstruction of the plant is presented. Based on unique leaf morphology, these fossil plants are clearly not assignable to the genus Pistia and are described as Cobbania corrugata (Lesquereux) Stockey, Rothwell et Johnson gen. et comb. nov. Recent systematic analyses using molecular characters resolve two separate origins of floating aquatic aroids included in the duckweeds and the genus Pistia. This new fossil genus increases our understanding of colonization of aquatic habitats by revealing a third possible origin of the floating aquatic habit within Araceae. PMID:21636430

  5. [Geoalkalibacter ferrihydriticus gen. nov., sp. nov., the first alkaliphilic representative of the family Geobacteraceae, isolated from a soda lake].

    PubMed

    Zavarzina, D G; Kolganova, T V; Bulygina, E S; Kostrikina, N A; Turova, T P; Zavarzin, G A

    2006-01-01

    Investigation of iron reduction in bottom sediments of alkaline soda lakes resulted in the isolation of a new obligately anaerobic iron-reducing bacterium, strain Z-0531, from Lake Khadyn (Tuva Republic, Russia) sediment samples. The cells of strain Z-0531 are short (1.0-1.5 by 0.3-0.5 microm), motile, non-spore-forming, gram-negative rods. The isolate is an obligate alkaliphile, developing in the pH range of 7.8-10.0, with an optimum at pH 8.6. It does not require NaCl but grows at NaCl concentrations of 0-50 g/1l. It can oxidize acetate with such electron acceptors as amorphous Fe(llI) hydroxide (AFH), EDTA-Fe(III), anthraquinone-2,6-disulfonate (quinone), Mn(IV), and S(0). On media with EDTA-Fe(III), the isolate can oxidize, apart from acetate, ethanol, pyruvate, oxalate, arginine, tartrate, lactate, propionate, and serine. H2 is not utilized. The reduced products formed during growth with AFH are siderite or magnetite, depending on the growth conditions. The isolate is incapable of fermenting sugars, peptides, and amino acids. Yeast extract or vitamins are required as growth factors. The organism is capable of dinitrogen fixation and harbors the nifH gene. The DNA G+C content is 55.3 mol %. 16S rRNA analysis places strain Z-0531 into the family Geobacteraceae. Its closest relative (93% similarity) is Desulfuromonas palmitatis. Based on phenotypic distinctions and phylogenetic position, it is proposed that strain Z-0531 be assigned to the new genus and species Geoalkalibacter ferrihydriticus gen. nov., sp. nov. PMID:17205802

  6. A new Late Cretaceous ginkgoalean reproductive structure Nehvizdyella gen. nov. from the Czech Republic and its whole-plant reconstruction.

    PubMed

    Kvacek, Jirí; Falcon-Lang, Howard J; Dasková, Jirina

    2005-12-01

    During the Mesozoic Era, gingkoaleans comprised a diverse and widespread group. Here we describe ginkgoalean fossils in their facies context from the Late Cretaceous (Cenomanian) Peruc-Korycany Formation of the Czech Republic and present a reconstruction of tree architecture and ecology. Newly described in this study is the ovuliferous reproductive structure, Nehvizdyella bipartita gen. et sp. nov. (Ginkgoales). This ovuliferous organ consists of a bifurcating axis, terminated by large cupule-like structures, probably homologous to the collar of the recent Ginkgo. Each cupule encloses an orthotropous ovule. In specimens with the early developmental stages preserved, the entire ovule and young seed, with the exception of the micropylar area, is embedded in the cupule. Mature seeds consist of sclerotesta and sarcotesta. Monosulcate pollen grains of Cycadopites-type are found adhering to the seeds. Although similar to Ginkgo in terms of its large size and reduced number of seeds, N. bipartita differs from the extant genus in having ovules completely enclosed in a cupule-like structure. The co-occurrence of N. bipartita with ginkgoalean leaves of Eretmophyllum obtusum (Velenovský) Kva?ek, J., ginkgoalean short shoots of Pecinovicladus kvacekii Falcon-Lang, and ginkgoalean trunk wood of Ginkgoxylon gruettii Pons and Vozenin-Serra in monodominant taphocoenoses at four geographically distant localities suggests that these remains all belong to one plant. This is supported by the close morphological and anatomical similarity between the different organs. Facies analysis of plant assemblages indicates that our Cretaceous tree occupied a water-stressed coastal salt marsh environment. It therefore represents the first unequivocal halophyte among the Ginkgoales. PMID:21646114

  7. Coprobacter fastidiosus gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from infant faeces.

    PubMed

    Shkoporov, Andrei N; Khokhlova, Ekaterina V; Chaplin, Andrei V; Kafarskaia, Lyudmila I; Nikolin, Alexei A; Polyakov, Vladimir Yu; Shcherbakova, Victoria A; Chernaia, Zoya A; Efimov, Boris A

    2013-11-01

    A novel obligately anaerobic, non-spore-forming, rod-shaped, non-motile Gram-reaction-negative bacterium was isolated from infant faeces. The strain, designated NSB1(T), was able to grow on rich media at 30-37 °C, in the presence of up to 2?% (w/v) Oxgall and 2?% (w/v) NaCl. Cells of strain NSB1(T) produced catalase, but not urease and indole. Aesculin was not hydrolysed. The strain was able to utilize d-glucose, lactose, maltose, mannose and raffinose as electron donors. When grown on d-glucose, the main metabolic end products were propionic and acetic acids, with a minor product being succinic acid. The major cellular fatty acids, iso-C15?:?0 and anteiso-C15?:?0, were present at a 1?:?1 molar ratio. The major menaquinone was MK-11. The DNA G+C content was found to be 38.5 mol%. According to 16S rRNA gene sequence analysis strain NSB1(T) is a member of the family Porphyromonadaceae, phylum Bacteroidetes. The closest relatives of the strain were Barnesiella viscericola (88.2?% identity) and Barnesiella intestinihominis (87.4?% identity). On the basis of phenotypic and genotypic properties of strain NSB1(T) we conclude that this strain represent a novel species in a new genus within the family of Porphyromonadaceae for which the name Coprobacter fastidiosus gen. nov., sp. nov. is proposed. The type strain of the species is NSB1(T) (?=?DSM 26242(T),?=?VKM B-2743(T)). PMID:23771624

  8. Diagnostic value of an amplification method (Gen-Probe) compared with that of culture for diagnosis of tuberculosis.

    PubMed Central

    Vlaspolder, F; Singer, P; Roggeveen, C

    1995-01-01

    Five hundred fifty respiratory and nonrespiratory specimens from 340 patients were analyzed by comparing the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test (MTD) with conventional culture, which was the method of reference, for the detection of the Mycobacterium tuberculosis complex. After resolution of discrepant results by retesting the samples and reviewing the patients' clinical histories, a total of 60 respiratory specimens were MTD and culture positive, 347 were MTD and culture negative, 4 were MTD positive and culture negative, and 1 was MTD negative and culture positive. This results in a sensitivity of 98.4%, a specificity of 98.9%, and positive and negative predictive values of 93.8 and 99.7%, respectively. Repeatedly, clinicians asked to test specimens of nonpulmonary origin by MTD. Although, MTD is not approved for use with nonrespiratory specimens, the following results were shown. Sixty-one pleural exudate specimens showed disappointing results (sensitivity, 20%). However, MTD performed well with another 77 nonrespiratory specimens; 17 samples were positive and 57 samples were negative by both MTD and culture. No false-negative results were found by MTD. Three MTD-positive, culture-negative specimens had high sample relative light unit/cutoff relative light unit ratios, strongly suggesting true tuberculosis. Positive microscopy and positive culture with MTD-negative results occurred 12 times. Those cultures showed atypical mycobacteria 11 times and Actinomyces species once. The stability of the reagents in the MTD kit was also assessed by testing reagents, including the enzyme mixture, kept at -70 degrees C for at least 6 months. No loss of activity was seen. PMID:8567908

  9. Bounagaea algeriensis gen. nov., sp. nov., an extremely halophilic actinobacterium isolated from a Saharan soil of Algeria.

    PubMed

    Meklat, Atika; Bouras, Noureddine; Mokrane, Salim; Zitouni, Abdelghani; Schumann, Peter; Spröer, Cathrin; Klenk, Hans-Peter; Sabaou, Nasserdine

    2015-08-01

    A novel halophilic actinobacterium strain, designated H8(T), was isolated from a Saharan soil sample collected in El-Goléa, South Algeria. Strain H8(T) was identified as representing a new genus using a polyphasic taxonomic approach. Phylogenetic analysis revealed that strain H8(T) shared the highest degree of 16S rRNA gene sequence similarity with 'Mzabimyces algeriensis' DSM 46680(T) (93.0 %), Saccharopolyspora ghardaiensis DSM 45606(T) (91.2 %), Halopolyspora alba DSM 45976(T) (90.8 %) and Actinopolyspora mortivallis DSM 44261(T) (90.0 %). The strain was found to grow optimally at 28-35 °C, at pH 6.0-7.0, and in the presence of 15-25 % (w/v) NaCl. The substrate mycelium was observed to be well developed and fragmented in liquid medium and on solid medium. The aerial mycelium was observed to be moderately abundant and to form long chains with non-motile, smooth-surfaced and ovoid or spherical spores at maturity. The cell wall of strain H8(T) was found to contain meso-diaminopimelic acid. The whole-cell hydrolysates were found to mainly contain arabinose and galactose. The diagnostic phospholipid detected was phosphatidylcholine, and MK-9(H4), MK-9(H2) and MK-10(H2) were found to be the predominant menaquinones. The major cellular fatty acids were determined to be anteiso-C17:0 and iso-C15:0. The genomic DNA G+C content of strain H8(T) was determined to be 71.3 mol%. The genotypic and phenotypic data showed that the strain represents a novel genus and species, for which the name Bounagaea algeriensis gen. nov., sp. nov. is proposed, with the type strain H8(T) (=DSM 45966(T) = CECT 8470(T)). PMID:26050246

  10. Measurements of the neutron electric to magnetic form factor ratio GEn/GMn via the ^2H(\\vec{e},e'\\vec{n})^1H reaction to Q^2 = 1.45 (GeV/c)^2

    E-print Network

    Jefferson Laboratory E93-038 Collaboration; :; B. Plaster; A. Yu. Semenov

    2005-11-13

    We report values for the neutron electric to magnetic form factor ratio, GEn/GMn, deduced from measurements of the neutron's recoil polarization in the quasielastic 2H(\\vec{e},e'\\vec{n})1H reaction, at three Q^2 values of 0.45, 1.13, and 1.45 (GeV/c)^2. The data at Q^2 = 1.13 and 1.45 (GeV/c)^2 are the first direct experimental measurements of GEn employing polarization degrees of freedom in the Q^2 > 1 (GeV/c)^2 region and stand as the most precise determinations of GEn for all values of Q^2.

  11. A new genus and species of fish leeches Dolichobdella rubra, gen. n., sp. n., (Clitellata, Hirudinida, Piscicolidae) from the northern Sea ofJapan

    NASA Astrophysics Data System (ADS)

    Utevsky, Serge Y.; Chernyshev, Alexei V.

    2013-02-01

    A new species of fish leeches, Dolichobdella rubra gen. n., sp. n., was found in samples collected by RV Akademik M.A. Lavrentyev in the northern Sea of Japan from 470-528 m during the joint Russian-German expedition SoJaBio (Sea of Japan Biodiversity Studies) in August 2010. The leech does not exceed 13 mm in length and has the following morphological characteristics: body elongated, smooth, lacking gills and pulsatile vesicles; eyes and ocelli absent; coloration reddish; female gonopore larger than male one; 6pairs of testisacs; accessory glands, conductive tissue and copulatory area present; ovisacs short; bursa long; coelomic system reduced.

  12. Seeking consent to genetic and genomic research in a rural Ghanaian setting: A qualitative study of the MalariaGEN experience

    PubMed Central

    2012-01-01

    Background Seeking consent for genetic and genomic research can be challenging, particularly in populations with low literacy levels, and in emergency situations. All of these factors were relevant to the MalariaGEN study of genetic factors influencing immune responses to malaria in northern rural Ghana. This study sought to identify issues arising in practice during the enrolment of paediatric cases with severe malaria and matched healthy controls into the MalariaGEN study. Methods The study used a rapid assessment incorporating multiple qualitative methods including in depth interviews, focus group discussions and observations of consent processes. Differences between verbal information provided during community engagement processes, and consent processes during the enrolment of cases and controls were identified, as well as the factors influencing the tailoring of such information. Results MalariaGEN participants and field staff seeking consent were generally satisfied with their understanding of the project and were familiar with aspects of the study relating to malaria. Some genetic aspects of the study were also well understood. Participants and staff seeking consent were less aware of the methodologies employed during genomic research and their implications, such as the breadth of data generated and the potential for future secondary research. Moreover, trust in and previous experience with the Navrongo Health Research Centre which was conducting the research influenced beliefs about the benefits of participating in the MalariaGEN study and subsequent decision-making about research participation. Conclusions It is important to recognise that some aspects of complex genomic research may be of less interest to and less well understood by research participants and that such gaps in understanding may not be entirely addressed by best practice in the design and conduct of consent processes. In such circumstances consideration needs to be given to additional protections for participants that may need to be implemented in such research, and how best to provide such protections. Capacity building for research ethics committees with limited familiarity with genetic and genomic research, and appropriate engagement with communities to elicit opinions of the ethical issues arising and acceptability of downstream uses of genome wide association data are likely to be important. PMID:22747883

  13. A review of "The Variorum Edition of the Poetry of John Donne: The Holy Sonnets." by Gary A. Stringer gen. ed. 

    E-print Network

    Albert C. Labriola

    2006-01-01

    REVIEWS 1 Gary A. Stringer, gen. ed. The Variorum Edition of the Poetry of John Donne: The Holy Sonnets, Volume 7, Part 1. Bloomington: Indiana University Press, 2005. cvii + 606 pp. $59.95. Review by ALBERT C. LABRIOLA, DUQUESNE UNIVERSITY.... This volume, the fourth published in the projected eight-volume series, provides (1) new and authoritative texts of nineteen Holy Sonnets and (2) a synopsis of all commentary from the 1600s to the present era. On both counts, this volume, which the MLA has...

  14. The EU FP6 EpiGenChlamydia Consortium: contribution of molecular epidemiology and host-pathogen genomics to understanding Chlamydia trachomatis-related disease.

    PubMed

    Morré, S A; Ouburg, S; Peña, A S; Brand, A

    2009-11-01

    Chlamydia trachomatis infections are responsible for the world's leading cause of blindness (trachoma) and its most prevalent sexually transmitted disease, which is strongly associated with pelvic inflammatory disease, ectopic pregnancy and tubal infertility. Twin study-based findings of members of EpiGenChlamydia Consortium estimate that there is a 40% genetic predisposition to C. trachomatis infections. It is likely that the advances in human genomics will help to unravel the genetic predisposition at the gene level and will help to define a genetic fingerprint that can be used as a marker for this predisposition. The information gathered to date suggests that this predisposition and the factors contributing to prognosis are multifactorial. The EpiGenChlamydia Consortium aims to structure transnational research to such a degree that comparative genomics and genetic epidemiology can be performed in large numbers of unrelated individuals. Biobanking and data-warehouse building are the most central deliverables of the Coordination Action of the Consortium in Functional Genomics Research. In addition, the collective synergy acquired in this Coordination Action will allow for the generation of scientific knowledge on the C. trachomatis-host interaction, knowledge on the genetic predisposition to C. trachomatis infection and the development of tools for early detection of a predisposition to C. trachomatis infection and its complications. This review summarizes the consortium aims and progress, and future perspectives and directions. PMID:20011689

  15. Effectiveness of a Cloning and Sequencing Exercise on Student Learning with Subsequent Publication in the National Center for Biotechnology Information GenBank

    PubMed Central

    Lau, Joann M.

    2009-01-01

    With rapid advances in biotechnology and molecular biology, instructors are challenged to not only provide undergraduate students with hands-on experiences in these disciplines but also to engage them in the “real-world” scientific process. Two common topics covered in biotechnology or molecular biology courses are gene-cloning and bioinformatics, but to provide students with a continuous laboratory-based research experience in these techniques is difficult. To meet these challenges, we have partnered with Bio-Rad Laboratories in the development of the “Cloning and Sequencing Explorer Series,” which combines wet-lab experiences (e.g., DNA extraction, polymerase chain reaction, ligation, transformation, and restriction digestion) with bioinformatics analysis (e.g., evaluation of DNA sequence quality, sequence editing, Basic Local Alignment Search Tool searches, contig construction, intron identification, and six-frame translation) to produce a sequence publishable in the National Center for Biotechnology Information GenBank. This 6- to 8-wk project-based exercise focuses on a pivotal gene of glycolysis (glyceraldehyde-3-phosphate dehydrogenase), in which students isolate, sequence, and characterize the gene from a plant species or cultivar not yet published in GenBank. Student achievement was evaluated using pre-, mid-, and final-test assessments, as well as with a survey to assess student perceptions. Student confidence with basic laboratory techniques and knowledge of bioinformatics tools were significantly increased upon completion of this hands-on exercise. PMID:19952101

  16. Revision of the genus Polymerus (Heteroptera: Miridae) in the Eastern Hemisphere. Part 1: Subgenera Polymerus, Pachycentrum subgen. nov. and new genus Dichelocentrum gen. nov.

    PubMed

    Gapon, D A

    2014-01-01

    The paper represents the first part of a series dealing with the Eastern Hemisphere species of the genus Polymerus Hahn, 1831 and includes a redescription of the genus and the nominative subgenus, and descriptions of Pachycentrum subgen. nov., P. (Polymerus) russatus sp. nov. and P. (Pachycentrum) unciniger sp. nov. The specific name P. funestus Reuter, 1906 is transferred from the subgenus Poeciloscytus Fieber, 1858 to the nominative subgenus and synonymised with P. pekinensis Horváth, 1901. New combinations for seven African, Indian, and Australian species are proposed: Charagochilus aureus (Ballard, 1927) comb. nov., Ch. bimaculatus (Poppius, 1910) comb. nov., Ch. consanguineus (Distant, 1904) comb. nov., Ch. flavipes (Distant, 1904) comb. nov., Ch. madagascariensis (Poppius, 1914) comb. nov., Ch. obscuratus (Poppius, 1914) comb. nov., Proboscidocoris solitus (Walker, 1873) comb. nov. The species Polymerus nitidus (Odhiambo, 1959) is returned to the genus Proboscidocoris. Five African and Arabian species are included in the new genus Dichelocentrum gen. nov.: D. alkadanum (Linnavuori & van Harten, 2005) comb. nov., D. flora (Linnavuori & van Harten, 2005) comb. nov., D. longirostre (Reuter, 1905) comb. nov., D. ornatifrons (Odhiambo, 1959) comb. nov. and D. transvaalicum sp. nov. The specific name Polymerus xerophilus Linnavuori, 1975 syn. nov. is synonymised with D. ornatifrons comb. nov. Key, diagnoses, data on distribution, and illustrations of the parameres, entirely inflated vesica and the gynatrium are provided for all recognised species from the subgenera Polymerus, Pachycentrum subgen. nov. and the genus Dichelocentrum gen. nov. PMID:24869745

  17. U.S. DOE FreedomCAR and Vehicle Technologies Advanced Technology Development Program for Lithium-Ion Batteries: Gen 2 Performance Evaluation Interim Report

    SciTech Connect

    Jon P. Christophersen; Chet Motloch; Ira D. Bloom; Vince Battaglia; Ganesan Nagasubramanian; Tien Q. Duong

    2003-02-01

    The Advanced Technology Development Program is currently evaluating the performance of the second generation of Lithium-ion cells (i.e., Gen 2 cells). The 18650-size Gen 2 cells consist of a baseline chemistry and one variant chemistry. These cells were distributed over a matrix consisting of three states-of-charge (SOC) (60, 80, and 100% SOC), four temperatures (25, 35, 45, and 55°C), and three life tests (calendar-, cycle-, and accelerated-life). The calendar-life cells are clamped at an opencircuit voltage corresponding to 60% SOC and undergo a once-per-day pulse profile. The cycle-life cells are continuously pulsed using a profile that is centered around 60% SOC. The accelerated-life cells are following the calendar-life test procedures, but using the cycle-life pulse profile. Life testing is interrupted every four weeks for reference performance tests (RPTs), which are used to quantify changes in capacity, resistance, and power. The RPTs consist of a C1/1 and C1/25 static capacity tests, a low-current hybrid pulse power characterization test, and electrochemical impedance spectroscopy at 60% SOC. Capacity-, power-, and electrochemical impedance spectroscopy-based performance results are reported.

  18. Mangrovibacterium diazotrophicum gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove sediment, and proposal of Prolixibacteraceae fam. nov.

    PubMed

    Huang, Xiao-Fang; Liu, Yu Juan; Dong, Jun-De; Qu, Ling-Yun; Zhang, Yan-Ying; Wang, Fa-Zuo; Tian, Xin-Peng; Zhang, Si

    2014-03-01

    A nitrogen-fixing bacterium, designated strain SCSIO N0430(T), was isolated from a mangrove sediment sample. Analysis of the sequence of the nifH gene responsible for nitrogen fixation in this strain indicated a close relationship to an uncultured bacterium ZNZ-D11 (GenBank accession no. JF896696). 16S rRNA gene sequence analysis revealed that this isolate had less than 93?% similarity to its closest relative, Sunxiuqinia elliptica DQHS4(T). A phylogenetic tree reconstructed based on 16S rRNA gene sequences revealed that strain SCSIO N0430(T) was a member of the phylum Bacteroidetes. Chemotaxonomic and physiological characteristics, including phospholipids and major fatty acids, readily distinguished the isolate from established members of the phylum Bacteroidetes. It is concluded that strain SCSIO N0430(T) represents a novel genus and species, for which the name Mangrovibacterium diazotrophicum gen. nov., sp. nov. is proposed, with the type strain of the species SCSIO N0430(T) (?=?KCTC 32129(T)?=?DSM 27148(T)?=?JCM 19152(T)). Based on phylogenetic characteristics and 16S rRNA gene signature nucleotide patterns, the three genera Sunxiuqinia, Prolixibacter and Mangrovibacterium are proposed to make up a novel family, Prolixibacteraceae fam. nov., in the order Bacteroidales. PMID:24271213

  19. Anaerosolibacter carboniphilus gen. nov., sp. nov., a strictly anaerobic iron-reducing bacterium isolated from coal-contaminated soil.

    PubMed

    Hong, Heeji; Kim, So-Jeong; Min, Ui-Gi; Lee, Yong-Jae; Kim, Song-Gun; Roh, Seong Woon; Kim, Jong-Geol; Na, Jeong-Geol; Rhee, Sung-Keun

    2015-05-01

    A strictly anaerobic, mesophilic, iron-reducing bacterial strain, IRF19(T), was isolated from coal-contaminated soil in the Republic of Korea. IRF19(T) cells were straight, rod-shaped, Gram-staining-negative and motile by means of flagella. The optimum pH and temperature for their growth were determined to be pH 7.5-8.0 and 40 °C, while the optimum range was pH 6.5-10.0 and 20-45 °C, respectively. Strain IRF19(T) did not require NaCl for growth but it tolerated up to 2?% (w/v). Growth was observed with yeast extract, d-glucose, d-fructose, d-ribose, d-mannitol, d-mannose, l-serine, l-alanine and l-isoleucine. Fe(III), elemental sulfur, thiosulfate and sulfate were used as electron acceptors. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain IRF19(T) is affiliated to the family Clostridiaceae and is most closely related to Salimesophilobacter vulgaris Zn2(T) (93.5?% similarity), Geosporobacter subterraneus VNs68(T) (93.2?%) and Thermotalea metallivorans B2-1(T) (92.3?%). The major cellular fatty acids of strain IRF19(T) were C14?:?0, iso-C15?:?0 and C16?:?0, and the profile was distinct from those of the closely related species. The major respiratory quinone of strain IRF19(T) was menaquinone MK-5 (V-H2). The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and two unknown polar lipids. The G+C content of the genomic DNA of strain IRF19(T) was determined to be 37.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic results, strain IRF19(T) is considered to represent a novel species of a novel genus of the family Clostridiaceae , for which we propose the name Anaerosolibacter carboniphilus gen. nov., sp. nov., with the type strain IRF19(T) (?=?KCTC 15396(T)?=?JCM 19988(T)). PMID:25701849

  20. Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylum Acidobacteria from geothermal soils.

    PubMed

    Crowe, M A; Power, J F; Morgan, X C; Dunfield, P F; Lagutin, K; Rijpstra, W I C; Rijpstra, I C; Vyssotski, G N S; Sinninghe Damste, J S; Houghton, K M; Ryan, J L J; Stott, M B

    2014-01-01

    An aerobic, thermophilic, moderately acidophilic non-spore-forming bacterium, strain K22(T), was isolated from geothermally heated soil at Mount Ngauruhoe, New Zealand. On the basis of 16S rRNA gene sequence similarity, K22(T) was shown to belong to subdivision 4 of the phylum Acidobacteria and to be most closely related to 'Candidatus Chloracidobacterium thermophilum' (86?%) and Blastocatella fastidiosa (86?%). Cells stained Gram-negative and were catalase and oxidase-positive. The major fatty acids detected were iso-C15?:?0, iso-C17?:?0, iso-C19?:?0 and iso-C21?:?0 when standard lipid extraction protocols were employed. Analysis of the total cell lipid acid hydrolysate also detected membrane-spanning and ether lipids, which made up approximately 40?% of the total membrane composition. These lipids included dicarboxylic (iso-diabolic) acid and the glyceryl ether of alkyl analogues of iso-C15?:?0 and iso-diabolic acid. The G+C content of the genomic DNA was 59.6 mol% and the primary respiratory quinone was MK-8. Strain K22(T) grew at 50-69 °C with an optimum temperature of 65 °C and at pH 4.1-7.8 with an optimum growth pH of 6.5. NaCl tolerance was up to 1?% (w/v). Cells displayed a chemoheterotrophic and obligately aerobic metabolism. Cells grew on nutrient broth, alginate, arabinose, Casamino acids, glucose, lactate, formate, mannose, sodium alginate, peptone, sucrose, tryptone, xanthan, xylan, xylose and yeast extract. Nitrogen sources included nitrate, ammonium, urea, yeast extract and Casamino acids, but not dinitrogen gas. The distinct phylogenetic position and the phenotypic characteristics separate strain K22(T) from all other members of the class Acidobacteria and indicate that it represents a novel species and genus, for which the name Pyrinomonas methylaliphatogenes gen. nov., sp. nov. is proposed. The type strain of the type species is K22(T) (?=?DSM 25857(T)?=?ICMP 18710(T)). PMID:24048862

  1. Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes.

    PubMed

    Anders, Heike; Dunfield, Peter F; Lagutin, Kirill; Houghton, Karen M; Power, Jean F; Mackenzie, Andrew D; Vyssotski, Mikhail; Ryan, Jason L J; Hanssen, Eric G; Moreau, John W; Stott, Matthew B

    2014-04-01

    A strictly aerobic, thermophilic, moderately acidophilic, non-spore-forming bacterium, strain P373(T), was isolated from geothermally heated soil at Waikite, New Zealand. Cells were filamentous rods, 0.2-0.4 µm in diameter and grew in chains up to 80 µm in length. On the basis of 16S rRNA gene sequence similarity, strain P373(T) was shown to belong to the family Chitinophagaceae (class Sphingobacteriia) of the phylum Bacteroidetes, with the most closely related cultivated strain, Chitinophaga pinensis UQM 2034(T), having 87.6?% sequence similarity. Cells stained Gram-negative, and were catalase- and oxidase-positive. The major fatty acids were i-15?:?0 (10.8?%), i-17?:?0 (24.5?%) and i-17?:?0 3-OH (35.2?%). Primary lipids were phosphatidylethanolamine, two unidentified aminolipids and three other unidentified polar lipids. The presence of sulfonolipids (N-acyl-capnines) was observed in the total lipid extract by mass spectrometry. The G+C content of the genomic DNA was 47.3 mol% and the primary respiratory quinone was MK-7. Strain P373(T) grew at 35-63 °C with an optimum temperature of 60 °C, and at pH 5.5-8.7 with an optimum growth pH of 7.3-7.4. NaCl tolerance was up to 5?% (w/v) with an optimum of 0.1-0.25?% (w/v). Cell colonies were non-translucent and pigmented vivid yellow-orange. Cells displayed an oxidative chemoheterotrophic metabolism. The distinct phylogenetic position and the phenotypic characteristics separate strain P373(T) from all other members of the phylum Bacteroidetes and indicate that it represents a novel species in a new genus, for which the name Thermoflavifilum aggregans gen. nov., sp. nov. is proposed. The type strain of the type species is P373(T) (?=?ICMP 20041(T)?=?DSM 27268(T)). PMID:24425740

  2. Larsenia salina gen. nov., sp. nov., a new member of the family Halomonadaceae based on multilocus sequence analysis.

    PubMed

    León, María José; Sánchez-Porro, Cristina; de la Haba, Rafael R; Llamas, Inmaculada; Ventosa, Antonio

    2014-10-01

    Two Gram-staining-negative, moderately halophilic bacteria, strains M1-18(T) and L1-16, were isolated from a saltern located in Huelva (Spain). They were motile, strictly aerobic rods, growing in the presence of 3-25% (w/v) NaCl (optimal growth at 7.5-10% [w/v] NaCl), between pH 4.0 and 9.0 (optimal at pH 6.0-7.0) and at temperatures between 15 and 40°C (optimal at 37°C). Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that both strains showed the higher similarity values with Chromohalobacter israelensis ATCC 43985(T) (95.2-94.8%) and Chromohalobacter salexigens DSM 3043(T) (95.0-94.9%), and similarity values lower than 94.6% with other species of the genera Chromohalobacter, Kushneria, Cobetia or Halomonas. Multilocus sequence analysis (MLSA) based on the partial sequences of atpA, rpoD and secA housekeeping genes indicated that the new isolates formed an independent and monophyletic branch that was related to the peripheral genera of the family Halomonadaceae, Halotalea, Carnimonas and Zymobacter, supporting their placement as a new genus of the Halomonadaceae. The DNA-DNA hybridization between both strains was 82%, whereas the values between strain M1-18(T) and the most closely related species of Chromohalobacter and Kushneria were equal or lower to 48%. The major cellular fatty acids were C18:1?7c/C18:1?6c, C16:0, and C16:1?7c/C16:1?6c, a profile that differentiate this new taxon from species of the related genera. We propose the placement of both strains as a novel genus and species, within the family Halomonadaceae, with the name Larsenia salina gen. nov., sp. nov. The type strain is M1-18(T) (=CCM 8464=CECT 8192(T)=IBRC-M 10767(T)=LMG 27461(T)). PMID:25180007

  3. Crenotalea thermophila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a hot spring.

    PubMed

    Hanada, Satoshi; Tamaki, Hideyuki; Nakamura, Kazunori; Kamagata, Yoichi

    2014-04-01

    A thermophilic aerobic bacterium designated strain STH-1-Y1(T) was isolated from sulfur-turf in a Japanese hot spring (Okuhodaka hot spring, Gifu Pref.). Colonies of strain STH-1-Y1(T) were yellow and low convex morphology with a slightly irregular fringe. Cells were slender long rods, 0.4-0.6 µm wide and 1.2-3.0 µm long. The isolate was an obligate aerophilic organism, and could not grow by fermentation or nitrate respiration. The isolate had a thermophilic trait, and could grow at 35-60 °C and pH 5.5-7.5; maximum growth occurred at 55 °C and pH 7.0 with a doubling time of 1.9 h. The Biolog and API tests suggested that strain STH-1-Y1(T) was able to use various sugars such as glucose, lactose, mannose, maltose, trehalose, cellobiose and sucrose, but could not use sugar alcohols other than glycerol, i.e. adonitol, arabitol, erythritol, inositol, mannitol, sorbitol and xylitol. Lactate and glutamate could be used, but other fatty acids, i.e. acetate, citrate, propionate and succinate could not. Gelatin, casein, starch and glycogen were hydrolysed, but neither chitin nor agar was degraded. Cells lacked flexirubin and showed oxidase and catalase activities. The major respiratory quinone was menaquinone-7 (MK-7), and major cellular fatty acids were iso-C15?:?0, iso-C17?:?0 3-OH, iso-C17?:?0 and anteiso-C15?:?0. No unsaturated fatty acids were detected. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain STH-1-Y1(T) was closely related to the family Chitinophagaceae within the phylum Bacteroidetes. However, the isolate was evenly distant from all members in this family with sequence similarities of 87-89?%. These significantly low sequence similarities strongly suggested that strain STH-1-Y1(T) represents a novel species in a new genus of the family Chitinophagaceae within the phylum Bacteroidetes. Based on phenotypic and phylogenetic characteristics, the name Crenotalea thermophila gen. nov., sp. nov. is proposed. The type strain of the type species is STH-1-Y1(T) (?=?JCM 11541(T)?=?DSM 14807(T)). PMID:24436064

  4. Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil.

    PubMed

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Senthilkumar, Murugaiyan; Pragatheswari, Dhandapani; Lee, Jung-Sook; Lee, Keun-Chul

    2015-02-01

    Three novel bacterial strains, designated Vu-144(T), Vu-7 and Vu-35, were isolated on minimal medium from rhizosphere soil of field-grown cowpea and subjected to a taxonomic study using a polyphasic approach. Cells of the strains were Gram-stain-negative, non-motile, non-spore-forming, coccoid rods, and formed non-pigmented colonies. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Vu-144(T) was affiliated with an uncultivated lineage of the phylum Bacteroidetes. Its closest phylogenetic neighbour was the recently described species Niastella populi, a member of the family Chitinophagaceae, with just 90.7 % sequence similarity to the type strain. The only isoprenoid quinone detected was menaquinone 7 (MK-7). The fatty acid profiles showed large amounts of iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G and minor amounts of summed feature 3 (C16 : 1?7c and/or iso-C15 : 0 2-OH), C16 : 0 and other fatty acids, allowing the differentiation of the strains from other genera. The G+C content of the genomic DNA of the three strains ranged from 43.1 to 44.3 mol%. In addition to phosphatidylethanolamine, the major polar lipids were three unidentified aminophospholipids (APL1-APL3), two unidentified phospholipids (PL1, PL2) and three unidentified lipids (UL1-UL3). Biochemical test patterns also differed from those of Niastella populi and members of other genera. All three isolates showed plant-growth-promoting properties, e.g. the ability to produce indole-3-acetic acid and NH3 and to solubilize phosphate, utilized 1-aminocyclopropane 1-carboxylate (ACC) as a sole source of nitrogen and possessed the ACC deaminase enzyme. The novel isolates readily colonized roots and stimulated growth of tomato and cowpea under glasshouse conditions. Inoculated plants showed a 45-60 % increase in dry matter weight with respect to uninoculated controls. On the basis of the evidence from our polyphasic study, isolate Vu-144(T) represents a novel genus and species in the family Chitinophagaceae, for which the name Arachidicoccus rhizosphaerae gen. nov., sp. nov. is proposed. The type strain of Arachidicoccus rhizosphaerae is Vu-144(T) (?= KCTC 22378(T)?= NCIMB 14473(T)). PMID:25404481

  5. Otariodibacter oris gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of pinnipeds.

    PubMed

    Hansen, Mie Johanne; Bertelsen, Mads Frost; Christensen, Henrik; Bojesen, Anders Miki; Bisgaard, Magne

    2012-11-01

    A total of 27 bacterial isolates from California sea lions and a walrus tentatively classified within the family Pasteurellaceae was further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, tentatively designated Bisgaard taxon 57. According to 16S rRNA gene sequences, the most closely related species with a validly published name was Bisgaardia hudsonensis and the most closely related species based on rpoB sequence comparison was Pasteurella multocida subsp. multocida; highest similarities between the isolates and the type strains of B. hudsonensis and P. multocida subsp. multocida were 95.0 and 88.2%. respectively. All isolates of Bisgaard taxon 57 exhibit the phenotypic characters of the family Pasteurellaceae. Members of Bisgaard taxon 57 can be separated from existing genera of the Pasteurellaceae by the following tests: positive reactions for catalase, oxidase, Voges-Proskauer and indole; no X- or V-factor dependency; and acid production from L-arabinose (slow), L-fucose, maltose and trehalose, but not from dulcitol, D-mannitol, D-mannose or sucrose. The main fatty acids of Bisgaard taxon 57 (CCUG 59994(T)) are C(14:0), C(16:0), C(16:1)?7c and the summed feature C(14:0) 3-OH/iso-C(16:1) I. This fatty acid profile is characteristic of members of the Pasteurellaceae. The quinone profile of Bisgaard taxon 57 (DSM 23800(T)) was similar to that of other genera in the Pasteurellaceae. The DNA G+C content of strain Baika1(T) is 36.2 mol%, which is at the lower end of the range for members of the family Pasteurellaceae. On the basis of both phylogenetic and phenotypic evidence, it is proposed that members of Bisgaard taxon 57 should be classified as representatives of a novel species in a new genus, Otariodibacter oris gen. nov., sp. nov. The type strain of Otariodibacter oris is Baika1(T) (=CCUG 59994(T)=DSM 23800(T)), which was isolated from the oral cavity of a healthy California sea lion in Copenhagen Zoo, Denmark, in 2007. PMID:22199211

  6. Halorubellus salinus gen. nov., sp. nov. and Halorubellus litoreus sp. nov., novel halophilic archaea isolated from a marine solar saltern.

    PubMed

    Cui, Heng-Lin; Mou, Yun-Zhuang; Yang, Xin; Zhou, Yu-Guang; Liu, Hong-Can; Zhou, Pei-Jin

    2012-02-01

    Two extremely halophilic archaeal strains GX3(T) and GX26(T) were isolated from the Gangxi marine solar saltern near the Weihai city of Shandong Province, China. Cells from the two strains were pleomorphic and stained Gram-negative, colonies were red-pigmented. Strains GX3(T) and GX26(T) were able to grow at 25-50 °C (optimum 37 °C), at 1.4-5.1M NaCl (optimum 3.1M), at pH 5.5-9.5 (optimum pH 7.0) and neither strain required Mg(2+) for growth. Cells lyse in distilled water and the minimal NaCl concentration to prevent cell-lysis was 8% (w/v). The major polar lipids of the two strains were PA (phosphatidic acid), PG (phosphatidylglycerol), PGP-Me (phosphatidylglycerol phosphate methyl ester) and three major glycolipids (GL1, GL2 & GL3) chromatographically identical to S-TGD-1 (sulfated galactosyl mannosy glucosyl diether), S-DGD-1 (sulfated mannosyl glucosyl diether), and DGD-1 (mannosyl glucosyl diether) respectively, an unidentified lipid (GL4) was also detected in strain GX26(T). Phylogenetic analysis based on 16S rRNA gene revealed that strain GX3(T) and strain GX26(T) formed a distinct clade with the closest relative, Haladaptatus paucihalophilus (89.9-92.4% and 90.4-92.7, respectively). The rpoB' gene similarities between strains GX3(T) and GX26(T), and between the two strains and the closest relative, Halorussus rarus TBN4(T) are 96.5%, 84.3% and 83.9%, respectively. The DNA G+C contents of strain GX3(T) and strain GX26(T) are 67.3 mol% and 67.2 mol%, respectively. The DNA-DNA hybridization value between strain GX3(T) and strain GX26(T) was 44%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain GX3(T) and strain GX26(T) represent two novel species in a new genus within the family Halobacteriaceae, Halorubellus salinus gen. nov., sp. nov. (type strain GX3(T)=CGMCC 1.10384(T)=JCM 17115(T)) and Halorubellus litoreus sp. nov. (type strain GX26(T)=CGMCC 1.10386(T)=JCM 17117(T)). PMID:21889861

  7. Morphology and molecular phylogeny of a marine interstitial tetraflagellate with putative endosymbionts: Auranticordis quadriverberis n. gen. et sp. (Cercozoa)

    PubMed Central

    Chantangsi, Chitchai; Esson, Heather J; Leander, Brian S

    2008-01-01

    Background Comparative morphological studies and environmental sequencing surveys indicate that marine benthic environments contain a diverse assortment of microorganisms that are just beginning to be explored and characterized. The most conspicuous predatory flagellates in these habitats range from about 20–150 ?m in size and fall into three major groups of eukaryotes that are very distantly related to one another: dinoflagellates, euglenids and cercozoans. The Cercozoa is a diverse group of amoeboflagellates that cluster together in molecular phylogenies inferred mainly from ribosomal gene sequences. These molecular phylogenetic studies have demonstrated that several enigmatic taxa, previously treated as Eukaryota insertae sedis, fall within the Cercozoa, and suggest that the actual diversity of this group is largely unknown. Improved knowledge of cercozoan diversity is expected to help resolve major branches in the tree of eukaryotes and demonstrate important cellular innovations for understanding eukaryote evolution. Results A rare tetraflagellate, Auranticordis quadriverberis n. gen. et sp., was isolated from marine sand samples. Uncultured cells were in low abundance and were individually prepared for electron microscopy and DNA sequencing. These flagellates possessed several novel features, such as (1) gliding motility associated with four bundled recurrent flagella, (2) heart-shaped cells about 35–75 ?m in diam., and (3) bright orange coloration caused by linear arrays of muciferous bodies. Each cell also possessed about 2–30 pale orange bodies (usually 4–5 ?m in diam.) that were enveloped by two membranes and sac-like vesicles. The innermost membrane invaginated to form unstacked thylakoids that extended towards a central pyrenoid containing tailed viral particles. Although to our knowledge, these bodies have never been described in any other eukaryote, the ultrastructure was most consistent with photosynthetic endosymbionts of cyanobacterial origin. This combination of morphological features did not allow us to assign A. quadriverberis to any known eukaryotic supergroup. Thus, we sequenced the small subunit rDNA sequence from two different isolates and demonstrated that this lineage evolved from within the Cercozoa. Conclusion Our discovery and characterization of A. quadriverberis underscores how poorly we understand the diversity of cercozoans and, potentially, represents one of the few independent cases of primary endosymbiosis within the Cercozoa and beyond. PMID:18647416

  8. Alkalitalea saponilacus gen. nov., sp. nov., an obligately anaerobic, alkaliphilic, xylanolytic bacterium from a meromictic soda lake.

    PubMed

    Zhao, Baisuo; Chen, Shulin

    2012-11-01

    A Gram-positive, obligately anaerobic, motile, slender, flexible rod, designated SC/BZ-SP2(T), was isolated from mixed alkaline water and sediment of Soap Lake, Washington State, USA. Strain SC/BZ-SP2(T) formed salmon to pink colonies and was alkaliphilic. The isolate grew at pH(35 °C) 7.5-10.5 (optimum pH(35 °C) 9.7), at 8-40 °C (optimum 35-37 °C) and with 0.35-1.38 M Na(+) (optimum 0.44-0.69 M Na(+)). The isolate utilized L-arabinose, D-ribose, D-xylose, D-fructose, D-mannose, D-galactose, cellobiose, maltose, sucrose, trehalose, sorbitol, xylan, malate and yeast extract as carbon and energy sources; best growth was observed with L-arabinose, cellobiose, maltose and trehalose. The major fermentation products from beechwood xylan were propionate and acetate. The dominant fatty acids were iso-C(15:0), anteiso-C(15:0), iso-C(17:0) 3-OH, C(17:0) 3-OH and C(15:0) 3-OH. The cell-wall sugars were ribose, xylose, galactose and glucose. Thiosulfate and sulfite could be reduced to sulfide. The genomic DNA G+C content was 39.5 ± 0.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SC/BZ-SP2(T) belonged to the family Marinilabiliaceae of the order Bacteroidales, class Bacteroidia. The most closely related strains were Alkaliflexus imshenetskii Z-7010(T) (91.8% 16S rRNA gene sequence similarity), Marinilabilia salmonicolor Cy s1(T) (91.0%) and Anaerophaga thermohalophila Fru22(T) (90.4%). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain SC/BZ-SP2(T) represents a novel species in a new genus of the family Marinilabiliaceae, for which the name Alkalitalea saponilacus gen. nov., sp. nov. is proposed. The type strain of Alkalitalea saponilacus is SC/BZ-SP2(T) (=ATCC BAA-2172(T) =DSM 24412(T)). PMID:22199219

  9. Analytical specificity and sensitivity of the APTIMA Combo 2 and APTIMA GC assays for detection of commensal Neisseria species and Neisseria gonorrhoeae on the Gen-Probe Panther instrument.

    PubMed

    Golparian, Daniel; Tabrizi, Sepehr N; Unemo, Magnus

    2013-02-01

    Genetic detection of Neisseria gonorrhoeae is replacing culture for increased diagnostic sensitivity. Specificity of several nucleic acid amplification tests is suboptimal. Herein, the Gen-Probe APTIMA Combo 2 and APTIMA GC assays had 100% specificity and 100% sensitivity after confirmatory testing, when testing 298 isolates of nongonococcal Neisseria and related species and 205 gonococcal isolates. PMID:23324980

  10. The yeast genus Tortispora gen. nov., description of Tortispora ganteri sp. nov., Tortispora mauiana f.a., sp. nov., Tortispora agaves f.a., sp. nov., Tortispora sangerardii f.a., sp. nov.,...

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We describe the yeast genus Tortispora gen. nov., an early diverging lineage in the Saccharomycetales that features the formation of helical ascospores. The genus is based on 16 strains resembling Candida caseinolytica that were isolated from necrotic plant tissue in warm regions of the New World. B...

  11. Next-Gen Video

    ERIC Educational Resources Information Center

    Arnn, Barbara

    2007-01-01

    This article discusses how schools across the US are using the latest videoconference and audio/video streaming technologies creatively to move to the next level of their very specific needs. At the Georgia Institute of Technology in Atlanta, the technology that is the backbone of the school's extensive distance learning program has to be…

  12. cocomore.gen

    E-print Network

    ... Very Nice Arcade Game/Like Pac/Man 1381 AMORTIZE/BAS X JBELTRAMO 870425 ... 1260 57 2 Desc: ANIMATED RAINDROP ON WATER 1186 RSDEMO. .... 568 ICONS/SYS X T.SMITH 860817 7560 29 2 Desc: ICONS FOR MCPAINT ...

  13. Next Gen Libraries

    ERIC Educational Resources Information Center

    Villano, Matt

    2006-01-01

    Keeping a history of peace studies. Cataloging audio and video broadcasts important to the Northwest. Digitizing images and other documents older than the state of California. All of these efforts are important steps toward preserving the history of the nation's development. Digital library initiatives are nothing new; the effort to digitize data…

  14. GenBank Home

    Science.gov Websites

    Manual NCBI News PubMed PubMed Central (PMC) PubMed Clinical Queries PubMed Health All Literature Resources... Proteins BioSystems BLAST (Basic Local Alignment Search Tool)...

  15. Genome-wide linkage and positional association analyses identify associations of novel AFF3 and NTM genes with triglycerides: the GenSalt study.

    PubMed

    Li, Changwei; Bazzano, Lydia A L; Rao, Dabeeru C; Hixson, James E; He, Jiang; Gu, Dongfeng; Gu, Charles C; Shimmin, Lawrence C; Jaquish, Cashell E; Schwander, Karen; Liu, De-Pei; Huang, Jianfeng; Lu, Fanghong; Cao, Jie; Chong, Shen; Lu, Xiangfeng; Kelly, Tanika N

    2015-03-20

    We conducted a genome-wide linkage scan and positional association study to identify genes and variants influencing blood lipid levels among participants of the Genetic Epidemiology Network of Salt-Sensitivity (GenSalt) study. The GenSalt study was conducted among 1906 participants from 633 Han Chinese families. Lipids were measured from overnight fasting blood samples using standard methods. Multipoint quantitative trait genome-wide linkage scans were performed on the high-density lipoprotein, low-density lipoprotein, and log-transformed triglyceride phenotypes. Using dense panels of single nucleotide polymorphisms (SNPs), single-marker and gene-based association analyses were conducted to follow-up on promising linkage signals. Additive associations between each SNP and lipid phenotypes were tested using mixed linear regression models. Gene-based analyses were performed by combining P-values from single-marker analyses within each gene using the truncated product method (TPM). Significant associations were assessed for replication among 777 Asian participants of the Multi-ethnic Study of Atherosclerosis (MESA). Bonferroni correction was used to adjust for multiple testing. In the GenSalt study, suggestive linkage signals were identified at 2p11.2?2q12.1 [maximum multipoint LOD score (MML) = 2.18 at 2q11.2] and 11q24.3?11q25 (MML = 2.29 at 11q25) for the log-transformed triglyceride phenotype. Follow-up analyses of these two regions revealed gene-based associations of charged multivesicular body protein 3 (CHMP3), ring finger protein 103 (RNF103), AF4/FMR2 family, member 3 (AFF3), and neurotrimin (NTM) with triglycerides (P = 4 × 10(-4), 1.00 × 10(-5), 2.00 × 10(-5), and 1.00 × 10(-7), respectively). Both the AFF3 and NTM triglyceride associations were replicated among MESA study participants (P = 1.00 × 10(-7) and 8.00 × 10(-5), respectively). Furthermore, NTM explained the linkage signal on chromosome 11. In conclusion, we identified novel genes associated with lipid phenotypes in linkage regions on chromosomes 2 and 11. PMID:25819087

  16. Urnaloricus gadi nov. gen. et nov. sp. (Loricifera, Urnaloricidae nov. fam.), an aberrant Loricifera with a viviparous pedogenetic life cycle.

    PubMed

    Heiner, Iben; Kristensen, Reinhardt Møbjerg

    2009-02-01

    A new species of Loricifera, Urnaloricus gadi nov. gen. et nov. sp., is described from the Faroe Bank, located Southwest of the Faroe Islands, North Atlantic. The new species does not fit into any known families of Loricifera and therefore it is grouped into a new family Urnaloricidae nov. fam. The new species is characterized by having a very complicated life cycle that involves a large cyst-like mega-larva, two reduced larval instars and the Higgins-larvae eating their maternal stage from within. An adult stage is missing. This form of reproduction is called viviparous pedogenesis and normally is found only in nematodes and insects. In the life cycle of Urnaloricidae nov. fam., there are two types of free-living larval stages: a Higgins-larva and a mega-larva. The latter is found in two different forms, a pre- and a cyst-forming mega-larva. Additionally, there are two reduced life history stages, the reduced larval stage (probably a postlarva) and the ghost-larval stage inside the cyst-forming mega-larva. The external morphology of the two forms of mega-larvae is much reduced, e.g., the introvert has only a few rows of scalids when compared with the Higgins-larva. The pre mega-larva is free-living and can sometimes be covered with coccoliths. Internally, a large ovary with a few oocytes, a digestive system, and an internal armature with retracted scalids are present. The pre mega-larva presumably molts into a cyst-forming mega-larva and thereby the ovary is now seen inside the cyst-forming mega-larva. The cyst-forming mega-larva has the same structures as in the pre mega-larva though here the scalids are protruded and there is a gonopore. Inside the cyst-forming mega-larva the ovary produces more oocytes and begins to fill out the entire lumen. At this stage the cyst-forming mega-larva molts first to the presumed postlarval stage, and then this stage molts to a ghost-larva. Hence, the ovary now matures inside the ghost-larva, which is surrounded by both the cuticle of the reduced postlarval stage and the cuticle of the cyst-forming mega-larva. The oocytes mature into eggs, and then into embryos and finally into Higgins-larvae while reabsorbing all the tissue of their maternal stage, the ghost-larva. During this maturation the cuticle of the cyst-forming mega-larva starts to harden and become cyst-like. The fully developed Higgins-larvae emerge through the gonopore of the cyst-forming mega-larva by penetrating the thin cuticles of the ghost-larva and the postlarva. The embryos have holoblastic radial cleavage and later a fluid-filled blastocoel is formed. The eggshells are extremely elastic; hence, they can become very elongated as the embryos mature into Higgins-larvae. PMID:18798249

  17. Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning

    PubMed Central

    An, Gary C.; Faeder, James R.

    2009-01-01

    Introduction Intracellular signaling/synthetic pathways are being increasingly extensively characterized. However, while these pathways can be displayed in static diagrams, in reality they exist with a degree of dynamic complexity that is responsible for heterogeneous cellular behavior. Multiple parallel pathways exist and interact concurrently, limiting the ability to integrate the various identified mechanisms into a cohesive whole. Computational methods have been suggested as a means of concatenating this knowledge to aid in the understanding of overall system dynamics. Since the eventual goal of biomedical research is the identification and development of therapeutic modalities, computational representation must have sufficient detail to facilitate this “engineering” process. Adding to the challenge, this type of representation must occur in a perpetual state of incomplete knowledge. We present a modeling approach to address this challenge that is both detailed and qualitative. This approach is termed “dynamic knowledge representation,” and is intended to be an integrated component of the iterative cycle of scientific discovery. Methods BioNetGen (BNG), a software platform for modeling intracellular signaling pathways, was used to model the toll-like receptor 4 (TLR-4) signal transduction cascade. The informational basis of the model was a series of reference papers on modulation of (TLR-4) signaling, and some specific primary research papers to aid in the characterization of specific mechanistic steps in the pathway. This model was detailed with respect to the components of the pathway represented, but qualitative with respect to the specific reaction coefficients utilized to execute the reactions. Responsiveness to simulated lipopolysaccharide (LPS) administration was measured by tumor necrosis factor (TNF) production. Simulation runs included evaluation of initial dose-dependent response to LPS administration at 10, 100, 1000, and 10000, and a subsequent examination of preconditioning behavior with increasing LPS at 10, 100, 1000 and 10000 and a secondary dose of LPS at 10000 administered at ?27 h of simulated time. Simulations of “knockout” versions of the model allowed further examination of the interactions within the signaling cascade. Results The model demonstrated a dose-dependent TNF response curve to increasing stimulus by LPS. Preconditioning simulations demonstrated a similar dose-dependency of preconditioning doses leading to attenuation of response to subsequent LPS challenge—a “tolerance” dynamic. These responses match dynamics reported in the literature. Furthermore, the simulated “knockout” results suggested the existence and need for dual negative feedback control mechanisms, represented by the zinc ring-finger protein A20 and inhibitor kappa B proteins (I?B), in order for both effective attenuation of the initial stimulus signal and subsequent preconditioned “tolerant” behavior. Conclusions We present an example of detailed, qualitative dynamic knowledge representation using the TLR-4 signaling pathway, its control mechanisms and overall behavior with respect to preconditioning. The intent of this approach is to demonstrate a method of translating the extensive mechanistic knowledge being generated at the basic science level into an executable framework that can provide a means of “conceptual model verification.” This allows for both the “checking” of the dynamic consequences of a mechanistic hypothesis and the creation of a modular component of an overall model directed at the engineering goal of biomedical research. It is hoped that this paper will increase the use of knowledge representation and communication in this fashion, and facilitate the concatenation and integration of community-wide knowledge. PMID:18835283

  18. Description of Glaucomides bromelicola n. gen., n. sp. (Ciliophora, Tetrahymenida), a macrostome forming inhabitant of bromeliads (Bromeliaceae), including redescriptions of Glaucoma scintillans and G. reniformis.

    PubMed

    Foissner, Wilhelm

    2013-01-01

    Glaucomides bromelicola n. gen., n. sp. is a tetrahymenid ciliate common in tank bromeliads of Central and South America. The new genus is characterized by having a kinety fragment along the left mouth margin, an unciliated dorsolateral area, a tetrahymenid silverline pattern, and the ability to produce macrostomes when bacterial food is depleted. I provide a detailed description of the microstome and the macrostome morph, using several morphological methods. This showed that G. bromelicola does not belong to the Glaucomidae, but to the Bromeliophryidae. However, various morphological traits are highly similar to those of Glaucoma reniformis and G. scintillans, which are thus redescribed and compared with G. bromelicola. Most differences are inconspicuous, showing that new tetrahymenids must be described very carefully. The morphological and molecular data suggest a common ancestor for Glaucoma and Glaucomides, both performing their own radiation, the former in ordinary limnetic habitats, the latter in tank bromeliads. PMID:23347342

  19. Revision of the genus Pelecinobaccha Shannon, description of Relictanum gen. nov., and redescription of Atylobaccha flukiella (Curran, 1941) (Diptera: Syrphidae).

    PubMed

    Miranda, Gil Felipe Gonçalves; Marshall, Stephen A; Skevington, Jeffrey H

    2014-01-01

    Recent phylogenetic analyses of Ocyptamus Macquart, 1834 (Diptera, Syrphidae) confirmed the paraphyly of this genus and provided evidence to divide it into several monophyletic subgroups, of which the largest is the clade traditionally treated as the Ocyptamus tristis species group. This group is here redefined, divided into the genera Pelecinobaccha Shannon, 1927 and Relictanum gen. nov., and revised along with the closely related and newly resurrected genus Atylobaccha Hull, 1949. Twenty-four new species (22 in Pelecinobaccha and two in Relictanum) are described and 35 species (27 in Pelecinobaccha, seven in Relictanum and Atylobaccha flukiella Curran, 1941) are redescribed. Pelecinobaccha is divided into four species groups (P. adspersa species group, P. brevipennis species group, P. peruviana species group and P. susio species group). An identification key, illustrations and distribution maps for all species from this study are also presented. PMID:24943804

  20. Reclassification of Bacteriovorax marinus as Halobacteriovorax marinus gen. nov., comb. nov. and Bacteriovorax litoralis as Halobacteriovorax litoralis comb. nov.; description of Halobacteriovoraceae fam. nov. in the class Deltaproteobacteria.

    PubMed

    Koval, Susan F; Williams, Henry N; Stine, O Colin

    2015-02-01

    The taxonomic status of saltwater Bdellovibrio-like prokaryotic predators has been revised to assign species to Halobacteriovorax gen. nov. A reclassification of Bacteriovorax marinus as Halobacteriovorax marinus comb. nov. (type strain ATCC BAA-682(T)?= DSM 15412(T)) and Bacteriovorax litoralis as Halobacteriovorax litoralis comb. nov. (type strain ATCC BAA-684(T)?= DSM 15409(T)) is proposed. This revision is necessary because a previous proposal to retain saltwater isolates as species of Bacteriovorax and reclassify Bacteriovorax stolpii as Bacteriolyticum stolpii was not approved. The type species of a genus cannot be reassigned to another genus. Bacteriovorax stolpii is thus retained as the type species of Bacteriovorax and Halobacteriovorax marinus is the type species of Halobacteriovorax and of Halobacteriovoraceae fam. nov. PMID:25406234

  1. Proposal of a new halobacterial genus Natrinema gen. nov., with two species Natrinema pellirubrum nom. nov. and Natrinema pallidum nom. nov.

    PubMed

    McGenity, T J; Gemmell, R T; Grant, W D

    1998-10-01

    A phylogenetic analysis of 69 halobacterial 16S rRNA gene sequences has been carried out, integrating data from new isolates, previously described halobacteria and cloned sequences from uncultivated halobacteria. Halobacterium halobium NCIMB 777, Halobacterium trapanicum NCIMB 784 and Halobacterium salinarium NCIMB 786, together with several other strains (strains T5.7, L11 and Halobacterium trapanicum NCIMB 767) constitute a distinct lineage with at least 98.2% sequence similarity. These strains have been incorrectly assigned to the genus Halobacterium. Therefore, based on a variety of taxonomic criteria, it is proposed that Halobacterium salinarium NCIMB 786 is renamed as Natrinema pellirubrum nom. nov., the type species of the new genus Natrinema gen. nov., and that Halobacterium halobium NCIMB 777 and Halobacterium trapanicum NCIMB 784 are renamed as a single species, Natrinema pallidum nom. nov. It was notable that halobacteria closely related to the proposed new genus have been isolated from relatively low-salt environments. PMID:9828420

  2. Cryobacterium psychrophilum gen. nov., sp. nov., nom. rev., comb. nov., an obligately psychrophilic actinomycete to accommodate "Curtobacterium psychrophilum" Inoue and Komagata 1976.

    PubMed

    Suzuki, K; Sasaki, J; Uramoto, M; Nakase, T; Komagata, K

    1997-04-01

    "Curtobacterium psychrophilum," proposed by Inoue and Komagata in 1976, is a psychrophilic gram-positive irregular rod isolated from Antarctic soil. This organism grew optimally at 9 to 12 degrees C and did not grow at higher than 18 degrees C. Chemotaxonomic characteristics of this organism were the presence of 2,4-diaminobutyric acid in the cell wall and menaquinone-10 as the predominant respiratory quinone. The cellular fatty acid profile, which contained a significant amount of an anteiso-branched monounsaturated acid, 12-methyl tetradecenoic acid, was a distinctive characteristic of this organism and was reasonable for adaptation to low temperature. Phylogenetic analysis based on 16S ribosomal DNA sequences revealed that this organism was positioned at a separate branch in the family Microbacteriaceae, actinomycetes with group B peptidoglycan. We propose the name Cryobacterium psychrophilum gen. nov., sp. nov. for this organism. The type strain is JCM 1463 (= IAM 12024 = ATCC 43563 = IFO 15735 = NCIMB 2068). PMID:9103638

  3. Sylphella puccoon gen. n., sp. n. and two additional new species of aquatic oligochaetes (Lumbriculidae, Clitellata) from poorly-known lotic habitats in North Carolina (USA)

    USGS Publications Warehouse

    Rodriguez, Pilar; Fend, Steven V.; Lenat, David R.

    2014-01-01

    Three new species of Lumbriculidae were collected from floodplain seeps and small streams in southeastern North America. Some of these habitats are naturally acidic. Sylphella puccoon gen. n., sp. n. has prosoporous male ducts in X-XI, and spermathecae in XII-XIII. Muscular, spherical atrial ampullae and acuminate penial sheaths distinguish this monotypic new genus from other lumbriculid genera having similar arrangements of reproductive organs. Cookidrilus pocosinus sp. n. resembles its two subterranean, Palearctic congeners in the arrangement of reproductive organs, but is easily distinguished by the position of the spermathecal pores in front of the chaetae in X-XIII. Stylodrilus coreyi sp. n. differs from congeners having simple-pointed chaetae and elongate atria primarily by the structure of the male duct and the large clusters of prostate cells. Streams and wetlands of Southeastern USA have a remarkably high diversity of endemic lumbriculids, and these poorly-known invertebrates should be considered in conservation efforts.

  4. Air-Cooled Stack Freeze Tolerance Freeze Failure Modes and Freeze Tolerance Strategies for GenDriveTM Material Handling Application Systems and Stacks Final Scientific Report

    SciTech Connect

    Hancock, David, W.

    2012-02-14

    Air-cooled stack technology offers the potential for a simpler system architecture (versus liquid-cooled) for applications below 4 kilowatts. The combined cooling and cathode air allows for a reduction in part count and hence a lower cost solution. However, efficient heat rejection challenges escalate as power and ambient temperature increase. For applications in ambient temperatures below freezing, the air-cooled approach has additional challenges associated with not overcooling the fuel cell stack. The focus of this project was freeze tolerance while maintaining all other stack and system requirements. Through this project, Plug Power advanced the state of the art in technology for air-cooled PEM fuel cell stacks and related GenDrive material handling application fuel cell systems. This was accomplished through a collaborative work plan to improve freeze tolerance and mitigate freeze-thaw effect failure modes within innovative material handling equipment fuel cell systems designed for use in freezer forklift applications. Freeze tolerance remains an area where additional research and understanding can help fuel cells to become commercially viable. This project evaluated both stack level and system level solutions to improve fuel cell stack freeze tolerance. At this time, the most cost effective solutions are at the system level. The freeze mitigation strategies developed over the course of this project could be used to drive fuel cell commercialization. The fuel cell system studied in this project was Plug Power's commercially available GenDrive platform providing battery replacement for equipment in the material handling industry. The fuel cell stacks were Ballard's commercially available FCvelocity 9SSL (9SSL) liquid-cooled PEM fuel cell stack and FCvelocity 1020ACS (Mk1020) air-cooled PEM fuel cell stack.

  5. Parastrombidinopsis shimi n. gen., n. sp. (Ciliophora: Choreotrichia) from the coastal waters of Korea: morphology and small subunit ribosomal DNA sequence.

    PubMed

    Kim, Jae Seong; Jeong, Hae Jin; Strüeder-Kypke, Michaela C; Lynn, Denis H; Kim, Sanghee; Kim, Jong Hyeok; Lee, Seung Hyeon

    2005-01-01

    The planktonic ciliate Parastrombidinopsis shimi n. gen., n. sp. is described from both living cells and quantitative protargol-stained (QPS) preparations and the sequence of the small subunit rDNA (SSU rDNA) is reported. This species is almost oval when the cells are alive; when stained, it is cylindrical for the upper two-fifths, half-bowl shaped for the middle two-fifths, and narrow rodshaped for the lower one-fifth. The ranges (and mean +/- standard deviation, n = 20) of cell length, cell width, and oral diameter of living cells were 112-221 microm (168 +/- 39), 88-176 microm (121 +/- 30), and 53-110 microm (80 +/- 14), respectively, while those of the QPS-stained specimens (n = 54) were 88-225 microm (162 +/- 29), 55-163 microm (102 +/- 19), and 53-98 microm (69 +/- 9), respectively. Thirty-six to 48 external oral polykinetids had cilia 25-40 microm long. However, unlike Strombidinopsis species sensu stricto, P. shimi has an external oral polykinetid zone that is an open circle. This species has two shorter polykinetids associated with the end of the oral polykinetid zone, deep in the oral cavity. Like Strombidinopsis species in the subclass Choreotrichia, 36-50 somatic kineties were equally spaced around the cell body and extended from the oral to the posterior regions with 68-105 dikinetids per kinety. Both kinetosomes of each kinetid bore cilia 3-10 microm long. Parastrombidinopsis shimi had 2 (1-4) ovoid macronuclei of 20-82 x 15-32 microm. When properly aligned, the sequence of the SSU rDNA of P. shimi (GenBank Accession No. AJ786648) was approximately 5% different from that of Strobilidium caudatum and 6% different from that of two Strombidinopsis species. Based both on morphology and gene sequence divergence, we establish this is as a new species in a new genus belonging to the family Strombidinopsidae. PMID:16313444

  6. A service evaluation of the Gen-Probe APTIMA nucleic acid amplification test for Trichomonas vaginalis: should it change whom we screen for infection?

    PubMed Central

    Hathorn, Emma; Ng, Andrea; Page, Matthew; Hodson, James; Gaydos, Charlotte; Ross, Jonathan D C

    2015-01-01

    Objective A service evaluation of the new Gen-Probe APTIMA nucleic acid amplification test was performed to determine the prevalence of Trichomonas vaginalis (TV) infection in a UK sexual health clinic and identify risk factors to inform an appropriate TV screening strategy. Method Unselected patients presenting with a new clinical episode were offered TV testing with Gen Probe transcription-mediated amplification (TV TMA) in addition to routine sexually transmitted infection screening. Asymptomatic females provided a self-collected vulvovaginal specimen and asymptomatic men a first-void urine sample. Symptomatic patients were examined and a urethral swab taken from men and two posterior vaginal swabs from females; one for culture and one for TV TMA testing. Demographic and clinical data were collected on all patients positive for TV infection and 100 randomly selected TV-negative controls. Results 3503 patients underwent TV TMA testing during the evaluation period. The prevalence of TV infection was 21/1483, 1.4% (95% CI 0.9% to 2.2%) in men and 72/2020, 3.6% (95% CI 2.8% to 4.5%) in women. The rate of TV positivity was higher in Black Caribbean patients compared with Caucasian patients (men 5.4% vs 0.1%, p<0.001; women 9.0% vs 1.2%, p<0.001). TV TMA detected an additional 16 infections (38%) in symptomatic women compared with culture. Conclusions While screening all patients with TV TMA will identify more TV infections, the UK prevalence remains low and this approach is unlikely to be cost effective. In addition to testing symptomatic patients, targeted testing of high-risk asymptomatic groups using TV TMA should be considered. PMID:25170162

  7. Re-examination of the taxonomic status of Enterobacter helveticus, Enterobacter pulveris and Enterobacter turicensis as members of the genus Cronobacter and their reclassification in the genera Franconibacter gen. nov. and Siccibacter gen. nov. as Franconibacter helveticus comb. nov., Franconibacter pulveris comb. nov. and Siccibacter turicensis comb. nov., respectively.

    PubMed

    Stephan, Roger; Grim, Christopher J; Gopinath, Gopal R; Mammel, Mark K; Sathyamoorthy, Venugopal; Trach, Larisa H; Chase, Hannah R; Fanning, Séamus; Tall, Ben D

    2014-10-01

    Recently, a taxonomical re-evaluation of the genus Enterobacter, based on multi-locus sequence typing (MLST) analysis, has led to the proposal that the species Enterobacter pulveris, Enterobacter helveticus and Enterobacter turicensis should be reclassified as novel species of the genus Cronobacter. In the present work, new genome-scale analyses, including average nucleotide identity, genome-scale phylogeny and k-mer analysis, coupled with previously reported DNA-DNA hybridization values and biochemical characterization strongly indicate that these three species of the genus Enterobacter are not members of the genus Cronobacter, nor do they belong to the re-evaluated genus Enterobacter. Furthermore, data from this polyphasic study indicated that all three species constitute two new genera. We propose reclassifying Enterobacter pulveris and Enterobacter helveticus in the genus Franconibacter gen. nov. as Franconibacter pulveris comb. nov. (type strain 601/05(T) = LMG 24057(T) = DSM 19144(T)) and Franconibacter helveticus comb. nov. (type strain 513/05(T) = LMG 23732(T) = DSM 18396(T)), respectively, and Enterobacter turicensis in the genus Siccibacter gen. nov. as Siccibacter turicensis comb. nov. (type strain 508/05(T) = LMG 23730(T) = DSM 18397(T)). PMID:25028159

  8. Atomic modelling of crystal/complex fluid/crystal contacts--Part II. Simulating AFM tests via the GenMol code for investigating the impact of CO2

    E-print Network

    Luquot, Linda

    a,n , J. Dweik b , P. Jouanna b , P. Gouze b , M. Andreani c , L. Luquot b a CINaM UPR-CNRS 3118 5570--ENS Lyon--UCB Lyon 1, France a r t i c l e i n f o Article history: Received 21 June 2010. Computer simulation A1. Interfaces B1. Mineral a b s t r a c t GenMolTM code is used to simulate Atomic

  9. Phase III multicenter trial comparing the efficacy of 2% dodecafluoropentane emulsion (EchoGen) and sonicated 5% human albumin (Albunex) as ultrasound contrast agents in patients with suboptimal echocardiograms

    Microsoft Academic Search

    Paul A Grayburn; James L Weiss; Terrence C Hack; Elizabeth Klodas; Joel S Raichlen; Manni A Vannan; Allan L Klein; Dalane W Kitzman; Steven G Chrysant; Jerald L Cohen; David Abrahamson; Elyse Foster; Julio E Perez; Gerard P Aurigemma; Julio A Panza; Michael H Picard; Benjamin F Byrd; Douglas S Segar; Stuart A Jacobson; David J Sahn; Anthony N DeMaria

    1998-01-01

    Objectives. This study was performed to compare the safety and efficacy of intravenous 2% dodecafluoropentane (DDFP) emulsion (EchoGen) with that of active control (sonicated human albumin [Albunex]) for left ventricular (LV) cavity opacification in adult patients with a suboptimal echocardiogram.Background. The development of new fluorocarbon-based echocardiographic contrast agents such as DDFP has allowed opacification of the left ventricle after peripheral

  10. Lachnoanaerobaculum gen. nov., a new genus in the Lachnospiraceae: characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of Eubacterium saburreum (Prevot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov.

    PubMed

    Hedberg, Maria E; Moore, Edward R B; Svensson-Stadler, Liselott; Hörstedt, Per; Baranov, Vladimir; Hernell, Olle; Wai, Sun Nyunt; Hammarström, Sten; Hammarström, Marie-Louise

    2012-11-01

    Two novel obligately anaerobic, Gram-stain-positive, saccharolytic and non-proteolytic spore-forming bacilli (strains CD3:22(T) and N1(T)) are described. Strain CD3:22(T) was isolated from a biopsy of the small intestine of a child with coeliac disease, and strain N1(T) from the saliva of a healthy young man. The cells of both strains were observed to be filamentous, approximately 5 to >20 µm long, some of them curving and with swellings. The novel organisms produced H(2)S, NH(3), butyric acid and acetic acid as major metabolic end products. Phylogenetic analyses, based on comparative 16S rRNA gene sequencing, revealed close relationships (98% sequence similarity) between the two isolates, as well as the type strain of Eubacterium saburreum and four other Lachnospiraceae bacterium-/E. saburreum-like organisms. This group of bacteria were clearly different from any of the 19 known genera in the family Lachnospiraceae. While Eubacterium species are reported to be non-spore-forming, reanalysis of E. saburreum CCUG 28089(T) confirmed that the bacterium is indeed able to form spores. Based on 16S rRNA gene sequencing, phenotypic and biochemical properties, strains CD3:22(T) and N1(T) represent novel species of a new and distinct genus, named Lachnoanaerobaculum gen. nov., in the family Lachnospiraceae [within the order Clostridiales, class Clostridia, phylum Firmicutes]. Strain CD3:22(T) (=CCUG 58757(T) =DSM 23576(T)) is the type strain of the type species, Lachnoanaerobaculum umeaense gen. nov., sp. nov., of the proposed new genus. Strain N1(T) (=CCUG 60305(T)=DSM 24553(T)) is the type strain of Lachnoanaerobaculum orale sp. nov. Moreover, Eubacterium saburreum is reclassified as Lachnoanaerobaculum saburreum comb. nov. (type strain CCUG 28089(T) =ATCC 33271(T) =CIP 105341(T) =DSM 3986(T) =JCM 11021(T) =VPI 11763(T)). PMID:22228654

  11. Hagleromyces gen. nov., a yeast genus in the Saccharomycetaceae, and description of Hagleromyces aurorensis sp. nov., isolated from water tanks of bromeliads.

    PubMed

    Sousa, Francisca M P; Morais, Paula B; Lachance, Marc-André; Rosa, Carlos A

    2014-08-01

    Three strains of a novel yeast species were isolated from water tanks (phytotelmata) of a bromeliad species collected in the state of Tocantins, Brazil. Analysis of sequences for the region spanning the SSU rRNA gene, the internal transcribed spacer, the 5.8S rRNA gene and the D1/D2 domains of the LSU rRNA gene and RNA polymerase II gene showed that these novel yeasts belong to a species that is distinct from all recognized ascomycetous yeast species. Based on the results of gene sequence analyses, a novel species representing a new genus in the Saccharomycetaceae is proposed. The novel species is assigned to the genus Hagleromyces gen. nov. The three isolates of the novel yeast species failed to form sexual spores alone or in mixtures. The name Hagleromyces aurorensis sp. nov. is proposed to accommodate these isolates. The type strain of H. aurorensis sp. nov. is UFMG-CM-Y311(T) (?=?CBS 13264(T)). PMID:24879649

  12. Cotterillia bromelicola nov. gen., nov. spec., a gonostomatid ciliate (Ciliophora, Hypotricha) from tank bromeliads (Bromeliaceae) with de novo originating dorsal kineties.

    PubMed

    Foissner, Wilhelm; Stoeck, Thorsten

    2011-01-01

    Cotterillia bromelicola nov. gen., nov. spec. was discovered in the tanks of the Mexican bromeliad Tillandsia heterophylla. Its morphology, ontogenesis, and 18S rDNA were studied with standard methods. Cotterillia has many cirral rows on both sides of the body. Uniquely, and thus used to diagnose the new genus Cotterillia, it has dorsal kineties originating de novo, producing neokinetal waves where the parental dorsal kineties reorganize to "combined rows", consisting of dorsal bristles anteriorly and of cirri posteriorly. Thus, up to four generations of bristles and cirri occur on the dorsal body surface. Cotterillia bromelicola has a gonostomatid body and adoral zone of membranelles, while the dense ciliature and the neokinetal waves resemble kahliellid hypotrichs. However, the de novo origin of anlage 1 and the molecular analyses show convincingly that Cotterillia belongs to the GonostomatidaeSmall and Lynn, 1985, for which an improved diagnosis is provided. Thus, neokinetal waves originated several times independently. The molecular differences between Trachelostyla, Gonostomum, and Cotterillia are small (? 5%) compared to their distinct morphologies and ontogeneses, suggesting that the 18S rDNA underestimates generic diversity. Our study emphasizes the need of combined morphological, ontogenetic, and molecular investigations to unravel the complex phylogeny and evolution of hypotrich ciliates. PMID:20971620

  13. Aureibacter tunicatorum gen. nov., sp. nov., a marine bacterium isolated from a coral reef sea squirt, and description of Flammeovirgaceae fam. nov.

    PubMed

    Yoon, Jaewoo; Adachi, Kyoko; Park, Sanghwa; Kasai, Hiroaki; Yokota, Akira

    2011-10-01

    Two aerobic, Gram-reaction-negative, golden-yellow pigmented and rod-shaped bacteria, designated strains A5Q-118(T) and A5Q-27, were isolated from an unidentified sea squirt that thrives in the coral reefs off the coast of Okinawa, Japan. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolates were affiliated with the family 'Flammeovirgaceae' of the phylum Bacteroidetes. Strains A5Q-118(T) and A5Q-27 shared 100?% sequence similarity with each other and showed <92?% similarity with other cultivated members of the family 'Flammeovirgaceae'. The novel isolates were phenotypically and physiologically different from strains described previously. The DNA G+C content was 35.5-36.2 mol%, MK-7 was the major menaquinone and iso-C(15?:?0) and C(16?:?1)?5c were the major fatty acids. Based on the results of this polyphasic taxonomic study, it was concluded that strains A5Q-118(T) and A5Q-27 represent a novel species in a new genus of the family 'Flammeovirgaceae', for which the name Aureibacter tunicatorum gen. nov., sp. nov. is proposed. Proposal for designation of the Flammeovirgaceae fam. nov. is also presented. The type strain of Aureibacter tunicatorum is A5Q-118(T) (?=?KCTC 23232(T) ?=?NBRC 107587(T)). PMID:21037036

  14. Cranial Anatomy of Wendiceratops pinhornensis gen. et sp. nov., a Centrosaurine Ceratopsid (Dinosauria: Ornithischia) from the Oldman Formation (Campanian), Alberta, Canada, and the Evolution of Ceratopsid Nasal Ornamentation

    PubMed Central

    Evans, David C.; Ryan, Michael J.

    2015-01-01

    The fossil record of ceratopsid dinosaurs between the occurrence of their proximate sister taxa in the Turonian and the beginning of their well-documented radiation from the late Campanian of North America onwards (approximately 90 and 77 Ma) is poor, with only seven taxa described from this early period in their evolution. We describe a new taxon of a highly adorned basal centrosaurine, Wendiceratops pinhornensis gen. et sp. nov., from the lower part of the Oldman Formation (middle Campanian, approximately 78-79 Ma), Alberta, Canada. Over 200 bones derived from virtually all parts of the skeleton, including multiple well-preserved specimens of the diagnostic parietosquamosal frill, were collected from a medium-density monodominant bonebed, making the new taxon one of the best-represented early ceratopsids. The new taxon is apomorphic in having epiparietals at loci 2 and 3 developed as broad-based, pachyostotic processes that are strongly procurved anterodorsally to overhang the posterior and lateral parietal rami, and an ischium with a broad, rectangular distal terminus. Although the morphology of the nasal is incompletely known, Wendiceratops is inferred to have a large, upright nasal horn located close to the orbits, which represents the oldest occurrence of this feature in Ceratopsia. Given the phylogenetic position of the new taxon within Centrosaurinae, a enlarged nasal horn is hypothesized to have arisen independently at least twice in ceratopsid evolution. PMID:26154293

  15. Comparison of Airborne and Ground-Based Function Allocation Concepts for NextGen Using Human-In-The-Loop Simulations

    NASA Technical Reports Server (NTRS)

    Wing, David J.; Prevot, Thomas; Murdoch, Jennifer L.; Cabrall, Christopher D.; Homola, Jeffrey R.; Martin, Lynne H.; Mercer, Joey S.; Hoadley, Sherwood T.; Wilson, Sara R.; Hubbs, Clay E.; Chamberlain, James P.; Chartrand, Ryan C.; Consiglio, Maria C.; Palmer, Michael T.

    2010-01-01

    This paper presents an air/ground functional allocation experiment conducted by the National Aeronautics and Space Administration (NASA) using two human-in-the-Loop simulations to compare airborne and ground-based approaches to NextGen separation assurance. The approaches under investigation are two trajectory-based four-dimensional (4D) concepts; one referred to as "airborne trajectory management with self-separation" (airborne) the other as "ground-based automated separation assurance" (ground-based). In coordinated simulations at NASA's Ames and Langley Research Centers, the primary operational participants -controllers for the ground-based concept and pilots for the airborne concept - manage the same traffic scenario using the two different 4D concepts. The common scenarios are anchored in traffic problems that require a significant increase in airspace capacity - on average, double, and in some local areas, close to 250% over current day levels - in order to enable aircraft to safely and efficiently traverse the test airspace. The simulations vary common independent variables such as traffic density, sequencing and scheduling constraints, and timing of trajectory change events. A set of common metrics is collected to enable a direct comparison of relevant results. The simulations will be conducted in spring 2010. If accepted, this paper will be the first publication of the experimental approach and early results. An initial comparison of safety and efficiency as well as operator acceptability under the two concepts is expected.

  16. Early experience with the NexGen® CR-Flex Mobile knee arthroplasty system: results of 2-year follow-up.

    PubMed

    Endres, Stefan; Wilke, Axel

    2010-03-20

    We evaluated our initial results in 57 patients who received the NexGen® CR-Flex Mobile knee system using the standard anterior approach in a prospective study. The bicondylar surface implant was cemented in position (Palacos®) without posterior patellar resurfacing. The clinical outcome and perioperative and post-operative complications were documented over 24 months of its use. Overall, after two years, good results were obtained for the categories of pain and ROM (range of motion), and for the HSS (knee society score) (pre-operative: 42/57; post-operative: 87/80). No pathological radiological findings were made during this period. Two patients, however, felt that the primary operation had not been successful because of lateral patellar tilt. This was corrected with revision surgery. It was remarkable that our patients achieved greater than 100° flexion within the first 14 days of the immediate post-operative period. Evaluation and comparison of the scores with those of conventional bicondylar surface replacement systems showed no relevant differences. PMID:21808697

  17. New evidence of the reproductive organs of Glossopteris based on permineralized fossils from Queensland, Australia. II: pollen-bearing organ Ediea gen. nov.

    PubMed

    Nishida, Harufumi; Pigg, Kathleen B; Kudo, Kensuke; Rigby, John F

    2014-03-01

    Ediea homevalensis H. Nishida, Kudo, Pigg & Rigby gen. et sp. nov. is proposed for permineralized pollen-bearing structures from the Late Permian Homevale Station locality of the Bowen Basin, Queensland, Australia. The taxon represents unisexual fertile shoots bearing helically arranged leaves on a central axis. The more apical leaves are fertile microsporophylls bearing a pair of multi-branched stalks on their adaxial surfaces that each supports a cluster of terminally borne pollen sacs. Proximal to the fertile leaves there are several rows of sterile scale-like leaves. The pollen sacs (microsporangia) have thickened and dark, striate walls that are typical of the Arberiella type found in most pollen organs presumed to be of glossopterid affinity. An examination of pollen organs at several developmental stages, including those containing in situ pollen of the Protohaploxypinus type, provides the basis for a detailed analysis of these types of structures, which bear similarities to both compression/impression Eretmonia-type glossopterid microsporangiate organs and permineralized Eretmonia macloughlinii from Antarctica. These fossils demonstrate that at least some Late Permian pollen organs were simple microsporophyll-bearing shoot systems and not borne directly on Glossopteris leaves. PMID:24165836

  18. Two new nematodes, Paraseuratoides ophisterni gen. et sp. n. (Quimperiidae) and Philometra ophisterni sp. n. (Philometridae), from the swamp-eel Ophisternon aenigmaticum in Mexico.

    PubMed

    Moravec, Frantisek; Salgado-Maldonado, Guillermo; Aguilar-Aguilar, Rogelio

    2002-01-01

    Two new nematodes, Paraseuratoides ophisterni gen. et sp. n. (Seuratoidea: Quimperiidae) and Philometra ophisterni sp. n. (Dracunculoidea: Philometridae) are described based on specimens recovered from the intestine and mesentery, respectively, of the swamp-eel Ophisternon aenigmaticum Rosen et Greenwood (Synbranchiformes: Synbranchidae) from a canal of the Papaloapan River in Tlacotalpan, State of Veracruz, Mexico. The genus Paraseuratoides is mot similar to Paraseuratum Johnston et Mawson, 1940, differing from it mainly in the absence of a bulbous inflation on the anterior end of the oesophagus and in the structure of the mouth (presence of 6 spines in addition to 6 oesophageal teeth). Neoquimperia Wang, Zhao, Wang et Zhang, 1979 and Wuinema Yu et Wang, 1992 are synonymised with Ezonema Boyce, 1971 and Paragendria Baylis, 1939, respectively, and Haplonema hamulatum Moulton, 1931 is considered a junior synonym of Ichthyobronema conoura Gnedina et Savina, 1930. Philometra ophisterni (only females) is mainly characterised by minute cephalic papillae, a greatly developed anterior oesophageal bulb separated from the cylindrical part of the oesophagus, anterior extension of the oesophageal gland anterior to the nerve ring, and by the character of large caudal projections. This is the first Philometra species recorded from inland fishes in Mexico. PMID:12194483

  19. Proposal of Effusibacillus lacus gen. nov., sp. nov., and reclassification of Alicyclobacillus pohliae as Effusibacillus pohliae comb. nov. and Alicyclobacillus consociatus as Effusibacillus consociatus comb. nov.

    PubMed

    Watanabe, Miho; Kojima, Hisaya; Fukui, Manabu

    2014-08-01

    A novel thermophilic, facultatively anaerobic bacterium, strain skLN1(T), was isolated from the sediment of a freshwater lake in Japan. Cells of strain skLN1(T) were rod-shaped and Gram-stain-variable. A KOH lysis test suggested that the cell wall of the isolate has a Gram-positive structure. For aerobic growth, the optimum pH was pH 7.25-7.50 and the optimum temperature was 50-52 °C. The G+C content of the genomic DNA was 50.8 mol%. Nitrate was reduced to nitrite. Alicyclic fatty acids were not detected, and branched-chain fatty acids were major components in the cellular fatty acid profile. MK-7 was the predominant respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolated strain was related most closely to Alicyclobacillus consociatus CCUG 53762(T) (95% similarity). This analysis also showed that the monophyly of the genus Alicyclobacillus had been lost. On the basis of phylogenetic and phenotypic characterization, Effusibacillus lacus gen. nov., sp. nov. is proposed. The type strain of Effusibacillus lacus is skLN1(T) (?=?NBRC 109614(T)?=?DSM 27172(T)). It is also proposed that Alicyclobacillus pohliae and Alicyclobacillus consociatus should be reclassified to the genus Effusibacillus as Effusibacillus pohliae comb. nov. and Effusibacillus consociatus comb. nov., respectively. PMID:24860109

  20. Characterization of Selenaion koniopes n. gen., n. sp., an amoeba that represents a new major lineage within heterolobosea, isolated from the Wieliczka salt mine.

    PubMed

    Park, Jong Soo; De Jonckheere, Johan F; Simpson, Alastair G B

    2012-01-01

    A new heterolobosean amoeba, Selenaion koniopes n. gen., n. sp., was isolated from 73‰ saline water in the Wieliczka salt mine, Poland. The amoeba had eruptive pseudopodia, a prominent uroid, and a nucleus without central nucleolus. Cysts had multiple crater-like pore plugs. No flagellates were observed. Transmission electron microscopy revealed several typical heterolobosean features: flattened mitochondrial cristae, mitochondria associated with endoplasmic reticulum, and an absence of obvious Golgi dictyosomes. Two types of larger and smaller granules were sometimes abundant in the cytoplasm--these may be involved in cyst formation. Mature cysts had a fibrous endocyst that could be thick, plus an ectocyst that was covered with small granules. Pore plugs had a flattened dome shape, were bipartite, and penetrated only the endocyst. Phylogenies based on the 18S rRNA gene and the presence of 18S rRNA helix 17_1 strongly confirmed assignment to Heterolobosea. The organism was not closely related to any described genus, and instead formed the deepest branch within the Heterolobosea clade after Pharyngomonas, with support for this deep-branching position being moderate (i.e. maximum likelihood bootstrap support--67%; posterior probability--0.98). Cells grew at 15-150‰ salinity. Thus, S. koniopes is a halotolerant, probably moderately halophilic heterolobosean, with a potentially pivotal evolutionary position within this large eukaryote group. PMID:22888835

  1. Description of Pseudobacteriovorax antillogorgiicola gen. nov., sp. nov., a bacterium isolated from the gorgonian octocoral Antillogorgia elisabethae, belonging to the family Pseudobacteriovoracaceae fam. nov., within the order Bdellovibrionales.

    PubMed

    McCauley, Erin P; Haltli, Brad; Kerr, Russell G

    2015-02-01

    A bacterial strain designated RKEM611(T) was isolated from the octocoral Antillogorgia elisabethae, collected off the coast of San Salvador, The Bahamas. The strain is Gram-stain-negative, an obligate aerobe, and pleomorphic. It requires NaCl for growth and exhibits optimal growth at 1-2 % (w/v) NaCl, 30-37 °C and pH 6.0-8.0. The predominant cellular fatty acids are C16 : 1?5c and C16 : 0; the major respiratory quinone is menaquinone MK-6, and the DNA G+C content is 46.3 mol%. Based on phylogenetic analysis of the 16S rRNA gene, in addition to phenotypic characteristics, RKEM611(T) represents a novel species and genus of a novel family within the order Bdellovibrionales. The names Pseudobacteriovoracaceae fam. nov. and Pseudobacteriovorax antillogorgiicola gen., nov., sp., nov. are proposed. Isolate RKEM611(T) (?= NCCB 100521(T)?= LMG 28452(T)) is the type strain. PMID:25389148

  2. A phylogenetic review of the North American band-winged grasshopper genus, Encoptolophus Scudder with description of Nebulatettix gen.n. (Orthoptera: Acrididae: Oedipodinae)

    PubMed Central

    Gómez, R. Antonio; Lightfoot, David C.; Miller, Kelly B.

    2014-01-01

    A taxonomic review of the North American band-winged grasshopper genus Encoptolophus Scudder (Orthoptera: Acrididae: Oedipodinae) was conducted. This genus is hypothesized to be non-monophyletic following a cladistic analysis of the genera in the Chortophaga genus group. We examined all species currently classified in this genus group for morphological characters and one behavioral character. The phenotypic character data were combined with three mitochondrial genes: cytochrome c oxidase subunit II, 16S rRNA and 12S rRNA. A parsimony analysis was performed on the combined data resulting in two equally parsimonious trees. Encoptolophus, as historically defined, is resolved in three separate clades. The results support erection of a new genus, Nebulatettix Gómez, Lightfoot & Miller gen.n. to comprise one of the groups historically classified in Encoptolophus. In addition, we transfer the species Encoptolophus californicus Bruner to Chimarocephala Scudder, comb.n., a combination used historically. The evolution of certain characters in the Chortophaga group is discussed, and a key to the genera is provided. PMID:24605044

  3. Molecular Phylogeny and Ultrastructure of Caliculium glossobalani n. gen. et sp. (Apicomplexa) from a Pacific Glossobalanus minutus (Hemichordata) Confounds the Relationships Between Marine and Terrestrial Gregarines.

    PubMed

    Wakeman, Kevin C; Reimer, James D; Jenke-Kodama, Holger; Leander, Brian S

    2014-01-01

    Gregarines are a diverse group of apicomplexan parasites with a conspicuous extracellular feeding stage, called a "trophozoite", that infects the intestines and other body cavities of invertebrate hosts. Although the morphology of trophozoites is very diverse in gregarines as a whole, high degrees of intraspecific variation combined with relatively low degrees of interspecific variation make the delimitation of different species based on trophozoite morphology observed with light microscopy difficult. The coupling of molecular phylogenetic data with comparative morphology has shed considerable light onto the boundaries and interrelationships of different gregarine species. In this study, we isolated a novel marine gregarine from the hepatic region of a Pacific representative of the hemichordate Glossobalanus minutus, and report the first ultrastructural and molecular data from any gregarine infecting this distinctive group of hosts. Molecular phylogenetic analyses of an SSU rDNA sequence derived from two single-cell isolates of this marine gregarine demonstrated a strong and unexpected affiliation with a clade of terrestrial gregarines (e.g. Gregarina). This molecular phylogenetic data combined with a comparison of the morphological features in previous reports of gregarines collected from Atlantic representatives of G. minutus justified the establishment of a new binomial for the new isolate, namely Caliculium glossobalani n. gen. et sp. The molecular phylogenetic analyses demonstrated a clade of terrestrial gregarines associated with a sequence acquired from a marine species, which suggest that different groups of terrestrial/freshwater gregarines evolved independently from marine ancestors. PMID:24702818

  4. Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3.

    PubMed

    Sorokin, Dimitry Y; Gumerov, Vadim M; Rakitin, Andrey L; Beletsky, Alexey V; Damsté, J S Sinninghe; Muyzer, Gerard; Mardanov, Andrey V; Ravin, Nikolai V

    2014-06-01

    Anaerobic enrichments from hypersaline soda lakes with chitin as substrate yielded five closely related anaerobic haloalkaliphilic isolates growing on insoluble chitin by fermentation at pH?10 and salinities up to 3.5?M. The chitinolytic activity was exclusively cell associated. To better understand the biology and evolutionary history of this novel bacterial lineage, the genome of the type strain ACht1 was sequenced. Analysis of the 2.6?Mb draft genome revealed enzymes of chitin-degradation pathways, including secreted cell-bound chitinases. The reconstructed central metabolism revealed pathways enabling the fermentation of polysaccharides, while it lacks the genes needed for aerobic or anaerobic respiration. The Rnf-type complex, oxaloacetate decarboxylase and sodium-transporting V-type adenosine triphosphatase were identified among putative membrane-bound ion pumps. According to 16S ribosomal RNA analysis, the isolates belong to the candidate phylum Termite Group 3, representing its first culturable members. Phylogenetic analysis using ribosomal proteins and taxonomic distribution analysis of the whole proteome supported a class-level classification of ACht1 most probably affiliated to the phylum Fibribacteres. Based on phylogenetic, phenotypic and genomic analyses, the novel bacteria are proposed to be classified as Chitinivibrio alkaliphilus gen. nov., sp. nov., within a novel class Chitinivibrione. PMID:24112708

  5. Isolation and characterization of a novel marine Bacteroidetes as Algitalea ulvae gen. nov., sp. nov., isolated from the green alga Ulva pertusa.

    PubMed

    Yoon, Jaewoo; Adachi, Kyoko; Kasai, Hiroaki

    2015-08-01

    A polyphasic taxonomic investigation was performed on a bacterial strain, 38-Ka-2(T), which was isolated from the green alga Ulva pertusa Kjellman (Chlorophyta) in Hokkaido, Japan. The bacterial cells were observed to be golden-yellow coloured, Gram-negative, strictly aerobic, non-spore-forming, non-motile and rod-shaped. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain is a member of the family Flavobacteriaceae within the phylum Bacteroidetes and that it shows high sequence similarity (94.8 %) to Aquimarina addita JC2680(T). The genomic DNA G+C content of strain 38-Ka-2(T) was determined to be 36 mol%; MK-6 was identified as the major menaquinone; and the presence of iso-C15:0, C18:0 and iso-C17:0 3-OH as the major (>10 %) cellular fatty acids. The polar lipid profile was found to consist of phosphatidylethanolamine, an unidentified glycolipid and two unidentified lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, strain 38-Ka-2(T) is considered to represent a novel genus for which the name Algitalea ulvae gen. nov., sp. nov. is proposed. The type strain of A. ulvae is 38-Ka-2(T) (=KCTC 32994(T) = NBRC 110017(T)). PMID:26063306

  6. Luteibaculum oceani gen. nov., sp. nov., a carotenoid-producing, lipolytic bacterium isolated from surface seawater, and emended description of the genus Owenweeksia Lau et al. 2005.

    PubMed

    Shahina, Mariyam; Hameed, Asif; Lin, Shih-Yao; Lai, Wei-An; Liu, You-Cheng; Hsu, Yi-Han; Young, Chiu-Chung

    2013-12-01

    A yellow-pigmented, Gram-staining-negative, strictly aerobic, rod-shaped, non-flagellated, non-spore-forming, lipolytic and gliding marine bacterium designated strain CC-AMWY-103B(T) was isolated from surface seawater collected at Kending, Taiwan. The strain shared the highest 16S rRNA gene sequence similarity of 89.4% with Owenweeksia hongkongensis JCM 12287(T) and Brumimicrobium mesophilum YH207(T), and established a distinct phyletic lineage associated with the members of the family Cryomorphaceae. The polar lipid profile of strain CC-AMWY-103B(T) consisted of phosphatidylethanolamine, ten unidentified lipids and four unidentified aminolipids. The major fatty acids (>5% of the total) were iso-C15?:?0, iso-C15?:?1 G, C15?:?1?5c, iso-C17?:?0 3-OH and C15?:?1?8c. The DNA G+C content was 44.2 ± 0.3 mol%. The predominant respiratory quinone was menaquinone-6 (MK-6) and the major polyamine was spermidine. Based on its genetic, phylogenetic, phenotypic and chemotaxonomic distinctiveness, strain CC-AMWY-103B(T) is proposed to represent a distinct member of the family Cryomorphaceae, for which the name Luteibaculum oceani gen. nov., sp. nov. is proposed; the type strain of Luteibaculum oceani is CC-AMWY-103B(T) (?=?JCM 18817(T)?=?BCRC 80551(T)). An emended description of the genus Owenweeksia is also proposed. PMID:23990655

  7. Savagea faecisuis gen. nov., sp. nov., a tylosin- and tetracycline-resistant bacterium isolated from a swine-manure storage pit.

    PubMed

    Whitehead, Terence R; Johnson, Crystal N; Patel, Nisha B; Cotta, Michael A; Moore, Edward R B; Lawson, Paul A

    2015-07-01

    A polyphasic taxonomic study using morphological, biochemical, chemotaxonomic and molecular methods was performed on three strains of a Gram-stain positive, non-sporeforming, motile aerobic rod-shaped bacterium resistant to tylosin and tetracycline isolated from a swine-manure storage pit. On the basis of 16S rRNA gene sequence analyses, it was confirmed that these isolates are highly related to each other and form a hitherto unknown lineage within the Planococcaceae. In particular, pairwise analysis of the 16S rRNA gene sequence demonstrated that the novel organism is closely related to members of the genus Sporosarcina (92.8-94.5 %), Pyschrobacillus (93.5-93.9 %) and Paenisporosarcina (93.3-94.5 %). The predominant fatty acids were found to consist of iso-C15:0 and iso-C17:1 ?10c and the G+C mol% was determined to be 41.8. Based on biochemical, chemotaxonomic, and phylogenetic evidence, it is proposed that these novel strains be classified as a novel genus and species, Savagea faecisuis gen nov., sp. nov. The type strain is Con12(T) (=CCUG 63563(T) = NRRL B-59945(T) = NBRC 109956(T)). PMID:25980832

  8. Description of Rummeliibacillus stabekisii gen. nov., sp. nov. and reclassification of Bacillus pycnus Nakamura et al. 2002 as Rummeliibacillus pycnus comb. nov.

    PubMed

    Vaishampayan, Parag; Miyashita, Mika; Ohnishi, Akihiro; Satomi, Masataka; Rooney, Alejandro; La Duc, Myron T; Venkateswaran, Kasthuri

    2009-05-01

    Strains of aerobic, Gram-positive, rod-shaped, round-spore-forming bacteria were isolated from different geographical locations and a subsequent polyphasic study was undertaken to clarify the taxonomic position of the round-spore-forming isolates strain KSC-SF6g(T), strain M32 and strain NBRC 12622. 16S rRNA gene sequence similarities demonstrated that these strains were most closely affiliated with Bacillus pycnus NRRL NRS-1691(T) (98 %), with species of Kurthia (96 %) and Viridibacillus (94-96 %) as the next nearest relatives. However, while DNA-DNA hybridization studies showed approx. 70 % reassociation among strains KSC-SF6g(T), M32 and NBRC 12622, DNA-DNA hybridization values between these strains and B. pycnus NRRL NRS-1691(T) never exceeded 13 %. Differences in the molecular structure of the cell-wall peptidoglycan could not differentiate these strains sufficiently from other closely related genera (Viridibacillus and Kurthia). However, Lys-Asp was present in strains KSC-SF6g(T), M32 and NBRC 12622, whereas l-Lys-d-Glu was reported in B. pycnus NRRL NRS-1691(T). The menaquinone MK-7 was dominant in strains KSC-SF6g(T), M32 and NBRC 12622 and members of the genus Kurthia, whereas MK-8 was abundant in Viridibacillus species. Strains KSC-SF6g(T), M32 and NBRC 12622 exhibited fatty acid profiles consisting of major amounts of anteiso-C(15 : 0) ( approximately 50 %) and iso-C(15 : 0) ( approximately 25 %) and moderate amounts of anteiso-C(17 : 0) ( approximately 7 %), which discriminated them from closely related B. pycnus NRRL NRS-1691(T) and species of Viridibacillus (iso-C(15 : 0); 46-74 %). The authors propose that strains KSC-SF6g(T), M32 and NBRC 12622 and B. pycnus NRRL NRS-1691(T) be reclassified into a separate genus based on clear-cut differences in discriminative taxonomic markers and the distant placement of B. pycnus and the novel strains described herein from other species of this clade according to current 16S rRNA gene sequence-based relatedness ( approximately 4 % difference in sequence). We propose the placement of these isolates into the novel genus Rummeliibacillus gen. nov. For the new taxon comprising strains KSC-SF6g(T), M32 and NBRC 12622, we propose the name Rummeliibacillus stabekisii gen. nov., sp. nov. (the type species of Rummeliibacillus), represented by the type strain KSC-SF6g(T) (=NRRL B-51320(T) =NBRC 104870(T)). In addition, Bacillus pycnus, which bears traits distinct from other round-spore-forming species [i.e. absence of growth at high NaCl (7 %), positive reaction for gelatin liquefaction], is reclassified as Rummeliibacillus pycnus comb. nov. (type strain JCM 11075(T) =NRRL NRS-1691(T)) based on phylogenetic affiliations and phenotypic characterization. PMID:19406799

  9. Chthoniobacter flavus gen. nov., sp. nov., the First Pure-Culture Representative of Subdivision Two, Spartobacteria classis nov., of the Phylum Verrucomicrobia

    PubMed Central

    Sangwan, Parveen; Chen, Xiaolei; Hugenholtz, Philip; Janssen, Peter H.

    2004-01-01

    The phylum Verrucomicrobia is increasingly recognized as an environmentally significant group of bacteria, particularly in soil habitats. At least six subdivisions of the Verrucomicrobia are resolved by comparative analysis of 16S rRNA genes, mostly obtained directly from environmental samples. To date, only two of these subdivisions (1 and 4) have characterized pure-culture representatives. We have isolated and characterized the first known pure-culture representative of subdivision 2. Strain Ellin428 is an aerobic heterotrophic bacterium that is able to grow with many of the saccharide components of plant biomass but does not grow with amino acids or organic acids other than pyruvate. Cells are yellow, rod-shaped, nonmotile, and gram-stain negative, and they contain peptidoglycan with direct cross-linkages of the A1? meso-Dpm type. The isolate grows well at 25°C on a variety of standard biological media, including some used in the routine cultivation of bacteria from soil. The pH range for growth is 4.0 to 7.0. Low levels of menaquinones MK-10 and MK-11 were detected. The major cellular fatty acids are C14:0, a-C15:0, C16:1?7c, and/or 2OH i-C15:0, and C16:0. The G+C content of the genomic DNA is 61 mol%. We propose a new genus and species, Chthoniobacter flavus gen. nov., sp. nov., with isolate Ellin428 as the type strain, and a new class for the subdivision to which it belongs, Spartobacteria classis nov. Environmental sequences indicate that the class Spartobacteria is largely represented by globally distributed, abundant, and active soil bacteria. PMID:15466527

  10. Thermicanus aegyptius gen. nov., sp. nov., Isolated from Oxic Soil, a Fermentative Microaerophile That Grows Commensally with the Thermophilic Acetogen Moorella thermoacetica

    PubMed Central

    Gößner, Anita S.; Devereux, Richard; Ohnemüller, Nadja; Acker, Georg; Stackebrandt, Erko; Drake, Harold L.

    1999-01-01

    A thermophilic, fermentative microaerophile (ET-5b) and a thermophilic acetogen (ET-5a) were coisolated from oxic soil obtained from Egypt. The 16S rRNA gene sequence of ET-5a was 99.8% similar to that of the classic acetogen Moorella thermoacetica. Further analyses confirmed that ET-5a was a new strain of M. thermoacetica. For ET-5b, the nearest 16S rRNA gene sequence similarity value to known genera was approximately 88%. ET-5b was found to be a motile rod with a genomic G+C content of 50.3 mol%. Cells were weakly gram positive and lacked spores. Growth was optimal at 55 to 60°C and pH 6.5 to 7.0. ET-5b grew under both oxic and anoxic conditions, but growth was erratic under atmospheric concentrations of O2. Utilizable substrates included oligosaccharides and monosaccharides. Acetate, formate, and succinate supported growth only under oxic conditions. Saccharides yielded succinate, lactate, ethanol, acetate, formate, and H2 under anoxic conditions; fermentation products were also formed under oxic conditions. A new genus is proposed, the type strain being Thermicanus aegyptius ET-5b gen. nov., sp. nov. (DSMZ 12793). M. thermoacetica ET-5a (DSMZ 12797) grew commensally with T. aegyptius ET-5b on oligosaccharides via the interspecies transfer of H2 formate, and lactate. In support of this interaction, uptake hydrogenase and formate dehydrogenase specific activities were fundamentally greater in M. thermoacetica ET-5a than in T. aegyptius ET-5b. These results demonstrate that (i) soils subject to high temperatures harbor uncharacterized thermophilic microaerophiles, (ii) the classic acetogen M. thermoacetica resides in such soils, and (iii) trophic links between such soil bacteria might contribute to their in situ activities. PMID:10543831

  11. Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs.

    PubMed

    Tavormina, Patricia L; Hatzenpichler, Roland; McGlynn, Shawn; Chadwick, Grayson; Dawson, Katherine S; Connon, Stephanie A; Orphan, Victoria J

    2015-01-01

    We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1(T), 'whale fall 1') that shares 98?% 16S rRNA gene sequence identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep-sea mussels, ?94.6?% 16S rRNA gene sequence identity with species of the genus Methylobacter and ?93.6?% 16S rRNA gene sequence identity with species of the genera Methylomonas and Methylosarcina. Strain WF1(T) represents the first cultivar from the 'deep sea-1' clade of marine methanotrophs, which includes members that participate in methane oxidation in sediments and the water column in addition to mussel endosymbionts. Cells of strain WF1(T) were elongated cocci, approximately 1.5 µm in diameter, and occurred singly, in pairs and in clumps. The cell wall was Gram-negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic DNA G+C content of WF1(T) was 40.5 mol%, significantly lower than that of currently described cultivars, and the major fatty acids were 16?:?0, 16?:?1?9c, 16?:?1?9t, 16?:?1?8c and 16?:?2?9,14. Growth occurred in liquid media at an optimal temperature of 23 °C, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1(T), a capacity that had not been functionally demonstrated previously in members of Methylobacter. On the basis of its unique morphological, physiological and phylogenetic properties, this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti gen. nov., sp. nov. The type strain of Methyloprofundus sedimenti is WF1(T) (?=?LMG 28393(T)?=?ATCC BAA-2619(T)). PMID:25342114

  12. Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991.

    PubMed

    Pankratov, Timofey A; Kirsanova, Lilia A; Kaparullina, Elena N; Kevbrin, Vadim V; Dedysh, Svetlana N

    2012-02-01

    A gram-negative, facultatively anaerobic, chemo-organotrophic, non-pigmented, slow-growing bacterium was isolated from acidic Sphagnum peat and designated strain TPB6017(T). Cells of this strain were long rods that multiplied by normal cell division and were motile by means of a single flagellum. Cells grew under reduced oxygen tension and under anoxic conditions and were able to ferment sugars and several polysaccharides, including amorphous and crystalline cellulose. Strain TPB6017(T) was a psychrotolerant acidophile capable of growth between pH 3.0 and 7.5 (optimum 4.5-5.0) and at 4-35 °C (optimum 20-28 °C). It was extremely sensitive to salt stress; growth was inhibited at NaCl concentrations above 0.1?% (w/v). The major fatty acids were iso-C(15?:?0) and iso-C(17?:?1)?9c; the polar lipids were phosphatidylethanolamine and a number of phospholipids and aminophospholipids with an unknown structure. The quinone was MK-8. The DNA G+C content was 57.6 mol%. Comparative 16S rRNA gene sequence analysis revealed that strain TPB6017(T) was a member of subdivision 1 of the phylum Acidobacteria and belonged to a phylogenetic lineage defined by the acidophilic aerobic chemo-organotroph Acidobacterium capsulatum (92.3?% sequence similarity). However, cell morphology, type of flagellation, the absence of pigment, differences in fatty acid and polar lipid composition, possession of a cellulolytic capability, inability to grow under fully oxic conditions and good growth in anoxic conditions distinguished strain TPB6017(T) from A. capsulatum. Therefore, it is proposed that strain TPB6017(T) represents a novel acidobacterium species in a new genus, Telmatobacter bradus gen. nov., sp. nov.; strain TPB6017(T) (?=?DSM 23630(T)?=?VKM B-2570(T)) is the type strain. PMID:21460138

  13. Genetics of recurrent early-onset depression (GenRED): design and preliminary clinical characteristics of a repository sample for genetic linkage studies.

    PubMed

    Levinson, Douglas F; Zubenko, George S; Crowe, Raymond R; DePaulo, Raymond J; Scheftner, William S; Weissman, Myrna M; Holmans, Peter; Zubenko, Wendy N; Boutelle, Sandra; Murphy-Eberenz, Kathleen; MacKinnon, Dean; McInnis, Melvin G; Marta, Diana H; Adams, Philip; Sassoon, Stephanie; Knowles, James A; Thomas, Jo; Chellis, Jennifer

    2003-05-15

    This is an initial report on a six-site collaborative project, Genetics of Recurrent Early-Onset Depression (GenRED). This is a study of a large sample of families with recurrent major depressive disorder (DSM-IV) beginning by the age 30 in probands or 40 in relatives. Evidence suggests that early onset and recurrence of depressive episodes predict substantially increased risk of depression in first-degree relatives compared with the general population, suggesting that susceptibility genes might be mapped with this phenotype. The projected sample of 800-1,000 affected sibling pairs (ASPs) and other relatives will be studied using genome scan methods. Biological materials and blinded clinical data will be made available through the NIMH cell repository program. The sample should have good-to-excellent power to detect a locus associated with a 24% or greater population-wide increase in risk to siblings. We describe 838 affected individuals from the first 305 families containing 434 independent ASPs, or 613 ASPs counting all possible pairs. The mean age at the onset was 18.5 years, with a mean of 7.3 episodes and longest episode of 655 days. Almost all subjects had experienced at least 4 weeks of depression with five or more additional symptom criteria. Frequencies of symptoms and psychiatric and medical comorbid are provided. Substance use was more common in males, and panic disorder in females. Within pairs of affected siblings, correlations were significant for age at onset, substance abuse/dependence, panic disorder, obsessive-compulsive disorder and nicotine initiation and persistence. We replicated previously reported associations among comorbid panic disorder and social phobia, chronicity of depression and suicidal behavior. This suggests comparability of our cases to those in earlier large family studies. This dataset should prove useful for genetic studies of a highly familial form of major depressive disorder. PMID:12707949

  14. Zhongshania antarctica gen. nov., sp. nov. and Zhongshania guokunii sp. nov., gammaproteobacteria respectively isolated from coastal attached (fast) ice and surface seawater of the Antarctic.

    PubMed

    Li, Hui-Juan; Zhang, Xi-Ying; Chen, Chun-Xiao; Zhang, Yan-Jiao; Gao, Zhao-Ming; Yu, Yong; Chen, Xiu-Lan; Chen, Bo; Zhang, Yu-Zhong

    2011-09-01

    Two Gram-negative, motile, aerobic, catalase- and oxidase-positive, rod-shaped strains, designated ZS5-23(T) and ZS6-22(T), were respectively isolated from Antarctic coastal attached (fast) ice and surface seawater samples. Both strains could grow at 4-35 °C (optimum 30 °C) and in the absence of NaCl. Analyses of 16S rRNA gene sequences revealed that strains ZS5-23(T) and ZS6-22(T) were closely related to each other (99.0?% sequence similarity) and belonged to the class Gammaproteobacteria, with their closest relatives being Spongiibacter and Melitea species (93.1-94.3?% sequence similarity). The predominant cellular fatty acids in both strains were C??:??8c, C??:? and summed feature 3 (C??:??7c and/or iso-C??:? 2-OH). Genomic DNA G+C contents of strains ZS5-23(T) and ZS6-22(T) were 51.5 and 51.8 mol%, respectively. The DNA-DNA relatedness between strains ZS5-23(T) and ZS6-22(T) was 50.9?%. Strains ZS5-23(T) and ZS6-22(T) could be differentiated from each other and from Spongiibacter and Melitea species by differences in a number of phenotypic properties. Based on the data presented, strains ZS5-23(T) and ZS6-22(T) represent two novel species in a new genus in the class Gammaproteobacteria, for which the names Zhongshania antarctica gen. nov., sp. nov. (the type species) and Zhongshania guokunii sp. nov. are proposed. The type strain of Zhongshania antarctica is ZS5-23(T) (?=?KACC 14066(T) ?=?CCTCC AB 209246(T)) and that of Zhongshania guokunii is ZS6-22(T) (?=?KACC 14532(T) ?=?CCTCC AB 209247(T)). PMID:20851909

  15. Halohasta litorea gen. nov. sp. nov., and Halohasta litchfieldiae sp. nov., isolated from the Daliang aquaculture farm, China and from Deep Lake, Antarctica, respectively.

    PubMed

    Mou, Yun-Zhuang; Qiu, Xing-Xing; Zhao, Mei-Lin; Cui, Heng-Lin; Oh, Dickson; Dyall-Smith, Mike L

    2012-11-01

    Two halophilic archaeal strains, R30(T) and tADL(T), were isolated from an aquaculture farm in Dailing, China, and from Deep Lake, Antarctica, respectively. Both have rod-shaped cells that lyse in distilled water, stain Gram-negative and form red-pigmented colonies. They are neutrophilic, require >120 g/l NaCl and 48-67 g/l MgCl(2) for growth but differ in their optimum growth temperatures (30 °C, tADL(T) vs. 40 °C, R30(T)). The major polar lipids were typical for members of the Archaea but also included a major glycolipid chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1). The 16S rRNA gene sequences of the two strains are 97.4 % identical, show most similarity to genes of the family Halobacteriaceae, and cluster together as a distinct clade in phylogenetic tree reconstructions. The rpoB' gene similarity between strains R30(T) and tADL(T) is 92.9 % and less to other halobacteria. Their DNA G + C contents are 62.4-62.9 mol % but DNA-DNA hybridization gives a relatedness of only 44 %. Based on phenotypic, chemotaxonomic and phylogenetic properties, we describe two new species of a novel genus, represented by strain R30(T) (= CGMCC 1.10593(T) = JCM 17270(T)) and strain tADL(T) (= JCM 15066(T) = DSMZ 22187(T)) for which we propose the names Halohasta litorea gen. nov., sp. nov. and Halohasta litchfieldiae sp. nov., respectively. PMID:23052830

  16. HPLC-DAD-Q-TOF-MS/MS analysis and HPLC quantitation of chemical constituents in traditional Chinese medicinal formula Ge-Gen Decoction.

    PubMed

    Yan, Yan; Chai, Cheng-Zhi; Wang, Da-Wei; Yue, Xin-Yi; Zhu, Dan-Ni; Yu, Bo-Yang

    2013-06-01

    Ge-Gen Decoction (GGD) is a classical formula of traditional Chinese medicine. It is generally used for treating common cold, fever and influenza in China and South East Asia. In this study, a systematic method was established for the qualitative and quantitative analysis of the major constituents in GGD. For qualitative analysis, a method of liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (Q-TOF MS/MS) was developed for identification of multi-constituents. Based on the UV spectra, retention time and MS spectra, sixty compounds in GGD extract were identified or tentatively characterized by comparing with reference substances or literatures. According to the qualitative results, a new quantitative analysis method of GGD was established by HPLC-DAD. Fourteen representative compounds unequivocally identified were chosen as marker components which were derived from five herbs in GGD excluding Zingiberis Rhizoma Recens and Jujubae Fructus. The analytical method was validated through intra- and inter-day precision, repeatability and stability, and the R.S.D. was less than 3.18%, 4.48%, 3.36% and 3.54%, respectively. The LODs and the LOQs for the analytes were less than 1.06 and 3.12?gmL(-1), respectively. The overall recoveries ranged from 94.8% to 105.6%, with the R.S.D. ranging from 0.68% to 3.23%. Then the new method was applied to determine twelve batches of GGD commercial products of three dosage forms. The results indicated that the new approach was applicable in the routine analysis and quality control of GGD products. The study might provide a basis for quality control of GGD, and further study of GGD in vivo. PMID:23584078

  17. Naumannella halotolerans gen. nov., sp. nov., a Gram-positive coccus of the family Propionibacteriaceae isolated from a pharmaceutical clean room and from food.

    PubMed

    Rieser, Gernot; Scherer, Siegfried; Wenning, Mareike

    2012-12-01

    Four Gram-stain-positive, aerobic bacterial strains isolated from a pharmaceutical clean room (strain WS4616(T)), a dessert milk product (strain WS4617) and from raw milk (strains WS4623 and WS4624) were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA and recA gene sequences showed that they formed a distinct lineage within the family Propionibacteriaceae. Similarity values between 16S rRNA gene sequences of the four novel strains and the type species of all genera belonging to the family Propionibacteriaceae were 89.2-94.1%. The major cellular fatty acid was anteiso-C(15:0) and the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Respiratory quinones were MK-8(H(4)) and MK-9(H(4)). The cell-wall peptidoglycan of type A3? contained ll-diaminopimelic acid, alanine, glycine and glutamic acid. The G+C content of the genomic DNA of strain WS4616(T) was 67.7 mol%. The whole-cell sugar pattern contained ribose, mannose, arabinose, glucose and galactose. On the basis of phenotypic and genetic data, strains WS4616(T), WS4617, WS4623 and WS4624 are classified as members of a novel species in a new genus of the family Propionibacteriaceae, for which the name Naumannella halotolerans gen. nov., sp. nov. is proposed. The type strain is WS4616(T) (?= DSM 24323(T) = LMG 26184(T)) and three additional strains are WS4617, WS4623 and WS4624. PMID:22307502

  18. Thermicanus aegyptius gen. nov., sp. nov., isolated from oxic soil, a fermentative microaerophile that grows commensally with the thermophilic acetogen Moorella thermoacetica.

    PubMed

    Gössner, A S; Devereux, R; Ohnemüller, N; Acker, G; Stackebrandt, E; Drake, H L

    1999-11-01

    A thermophilic, fermentative microaerophile (ET-5b) and a thermophilic acetogen (ET-5a) were coisolated from oxic soil obtained from Egypt. The 16S rRNA gene sequence of ET-5a was 99.8% similar to that of the classic acetogen Moorella thermoacetica. Further analyses confirmed that ET-5a was a new strain of M. thermoacetica. For ET-5b, the nearest 16S rRNA gene sequence similarity value to known genera was approximately 88%. ET-5b was found to be a motile rod with a genomic G+C content of 50.3 mol%. Cells were weakly gram positive and lacked spores. Growth was optimal at 55 to 60 degrees C and pH 6.5 to 7.0. ET-5b grew under both oxic and anoxic conditions, but growth was erratic under atmospheric concentrations of O(2). Utilizable substrates included oligosaccharides and monosaccharides. Acetate, formate, and succinate supported growth only under oxic conditions. Saccharides yielded succinate, lactate, ethanol, acetate, formate, and H(2) under anoxic conditions; fermentation products were also formed under oxic conditions. A new genus is proposed, the type strain being Thermicanus aegyptius ET-5b gen. nov., sp. nov. (DSMZ 12793). M. thermoacetica ET-5a (DSMZ 12797) grew commensally with T. aegyptius ET-5b on oligosaccharides via the interspecies transfer of H(2) formate, and lactate. In support of this interaction, uptake hydrogenase and formate dehydrogenase specific activities were fundamentally greater in M. thermoacetica ET-5a than in T. aegyptius ET-5b. These results demonstrate that (i) soils subject to high temperatures harbor uncharacterized thermophilic microaerophiles, (ii) the classic acetogen M. thermoacetica resides in such soils, and (iii) trophic links between such soil bacteria might contribute to their in situ activities. PMID:10543831

  19. A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera.

    PubMed

    Yoneda, Yasuko; Yoshida, Takashi; Yasuda, Hisato; Imada, Chiaki; Sako, Yoshihiko

    2013-10-01

    A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1(T), was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0-3.0 µm straight rods, often observed with round endospores. Strain KKC1(T) grew at 55-68 °C, pH 5.2-9.2 and 0.8-14?% (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0-7.5 and 2.46?% salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1(T) grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16?:?0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1(T) was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89?%. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1(T) (?=?DSM 26464(T)?=?NBRC 109353(T)). PMID:23606483

  20. Indirect determination of Li via 74Ge(n,?)75mGe activation reaction induced by neutrons from 7Li(p,n)7Be reaction

    NASA Astrophysics Data System (ADS)

    Kumar, Sanjiv; Reddy, G. L. N.; Rao, Pritty; Verma, Rakesh; Ramana, J. V.; Vikramkumar, S.; Raju, V. S.

    2012-03-01

    An indirect method to determine Li by 74Ge(n,?)75mGe activation reaction induced in a high purity Ge (detector) crystal by neutrons from the 7Li(p,n)7Be reaction in a typical particle-induced ?-ray emission (PIGE) spectroscopy experimental set-up is described. Performed with proton beams of energies in excess of 1.88 MeV, the threshold energy (Eth) of the 7Li(p,n)7Be reaction, the determination involves the activity measurement of 75mGe isotope that has a half-life of 47.7 s and decays with the emission of 139 keV ?-rays. Rapidity, selectivity and sensitivity down to ppm levels are the attractive features of the method. It is a suitable alternative to 7Li(p,p'?)7Li reaction based PIGE technique in the analyses of matrices that contain light elements such as Be, B, F, Na and Al in significant proportions. Interferences can arise from elements, for example V and Ti, that have Eth ? 1.88 MeV for (p,n) reaction. In the case of elements such as Cu, Mo which have with Eth > 1.88 MeV, the incident proton beam energy can be judiciously selected to avoid or minimize an interference. The method, under optimized irradiation conditions, does not entail a risk of neutron stimulated degradation of the performance of the detector. Besides analytical purposes, the measurement of the 75mGe activity can serve as a powerful tool to monitor even low (˜25 n/cm2 s) thermal neutron fluxes.

  1. Sonnenemertes cantelli gen. et sp. nov. (Heteronemertea)-A new Oxypolella-like nemertean from the abyssal plain adjacent to the Kuril-Kamchatka Trench

    NASA Astrophysics Data System (ADS)

    Chernyshev, Alexei V.; Abukawa, Shushi; Kajihara, Hiroshi

    2015-01-01

    Approximately 129 nemertean specimens were obtained in the material collected by the Russian-German KuramBio expedition 2012 to the abyssal plain adjacent to the Kuril-Kamchatka Trench (KKT). Due to deformed, fragmentary condition of most of the collected nemerteans they were identified to the order level only. Both archi- and heteronemerteans were very rare, and tubulanid palaeonemerteans and hoplonemerteans were predominant in the KuramBio epibenthic sledge (EBS) samples. Before the KuramBio expedition, only three species of the World fauna of benthic nemerteans had been known from depths exceeding 3000 m; according to data of Vityaz expedition in the KKT, published in 1955, unidentified nemerteans were found in all trawl samples from depths 1000 to 4640 m, but only one specimen of unidentified nemertean was collected from depths exceeding 5000 m. A reliable estimation of the actual species diversity of the present KuramBio samples could have been made primarily based on molecular genetic analyses; almost all the collected specimens are likely to represent undescribed species. In this study, a new species of the heteronemertean, Sonnenemertes cantelli gen. et sp. nov., from a depth of approximately 4870 m is described. This is the deepest record for an identified benthic nemertean, as well as the first species of the subfamily Oxypolellinae from the North Pacific. A single specimen was examined by light microscopy, scanning electron microscopy, and confocal laser scanning microscopy with phalloidin and antibody labeling. Morphologically, this species is similar to those in the genus Oxypolella. A preliminary molecular phylogenetic analysis based on partial 16S rDNA among the selected heteronemertean species indicated that S. cantelli formed a monophyletic group with Oxypolella alba Bergendal, 1903 together as a sister to the genus Baseodiscus. Systematic positioning of Oxypolella, Sonnenemertes, and related genera is discussed.

  2. Comparison of the GenMark Diagnostics eSensor Respiratory Viral Panel to Real-Time PCR for Detection of Respiratory Viruses in Children

    PubMed Central

    Pierce, Virginia M.

    2012-01-01

    A novel eSensor respiratory viral panel (eSensor RVP) multiplexed nucleic acid amplification test (GenMark Diagnostics, Inc., Carlsbad, CA) was compared to laboratory-developed real-time PCR assays for the detection of various respiratory viruses. A total of 250 frozen archived pediatric respiratory specimens previously characterized as either negative or positive for one or more viruses by real-time PCR were examined using the eSensor RVP. Overall agreement between the eSensor RVP and corresponding real-time PCR assays for shared analytes was 99.2% (kappa = 0.96 [95% confidence interval {CI}, 0.94 to 0.98]). The combined positive percent agreement was 95.4% (95% CI, 92.5 to 97.3); the negative percent agreement was 99.7% (95% CI, 99.4 to 99.8). The mean real-time PCR threshold cycle (CT) value for specimens with discordant results was 39.73 (95% CI, 38.03 to 41.43). Detection of coinfections and correct identification of influenza A virus subtypes were comparable between methods. Of note, the eSensor RVP rhinovirus assay was found to be more sensitive and specific than the corresponding rhinovirus real-time PCR. In contrast, the eSensor RVP adenovirus B, C, and E assays demonstrated some cross-reactivity when tested against known adenovirus serotypes representing groups A through F. The eSensor RVP is robust and relatively easy to perform, it involves a unique biosensor technology for target detection, and its multiplexed design allows for efficient and simultaneous interrogation of a single specimen for multiple viruses. Potential drawbacks include a slower turnaround time and the need to manipulate amplified product during the protocol, increasing the possibility of contamination. PMID:22875893

  3. Strategies to Avoid Wrongly Labelled Genomes Using as Example the Detected Wrong Taxonomic Affiliation for Aeromonas Genomes in the GenBank Database

    PubMed Central

    Beaz-Hidalgo, Roxana; Hossain, Mohammad J.; Liles, Mark R.; Figueras, Maria-Jose

    2015-01-01

    Around 27,000 prokaryote genomes are presently deposited in the Genome database of GenBank at the National Center for Biotechnology Information (NCBI) and this number is exponentially growing. However, it is not known how many of these genomes correspond correctly to their designated taxon. The taxonomic affiliation of 44 Aeromonas genomes (only five of these are type strains) deposited at the NCBI was determined by a multilocus phylogenetic analysis (MLPA) and by pairwise average nucleotide identity (ANI). Discordant results in relation to taxa assignation were found for 14 (35.9%) of the 39 non-type strain genomes on the basis of both the MLPA and ANI results. Data presented in this study also demonstrated that if the genome of the type strain is not available, a genome of the same species correctly identified can be used as a reference for ANI calculations. Of the three ANI calculating tools compared (ANI calculator, EzGenome and JSpecies), EzGenome and JSpecies provided very similar results. However, the ANI calculator provided higher intra- and inter-species values than the other two tools (differences within the ranges 0.06–0.82% and 0.92–3.38%, respectively). Nevertheless each of these tools produced the same species classification for the studied Aeromonas genomes. To avoid possible misinterpretations with the ANI calculator, particularly when values are at the borderline of the 95% cutoff, one of the other calculation tools (EzGenome or JSpecies) should be used in combination. It is recommended that once a genome sequence is obtained the correct taxonomic affiliation is verified using ANI or a MLPA before it is submitted to the NCBI and that researchers should amend the existing taxonomic errors present in databases. PMID:25607802

  4. Mucinivorans hirudinis gen. nov., sp. nov., an anaerobic, mucin-degrading bacterium isolated from the digestive tract of the medicinal leech Hirudo verbana.

    PubMed

    Nelson, Michael C; Bomar, Lindsey; Maltz, Michele; Graf, Joerg

    2015-03-01

    Three anaerobic bacterial strains were isolated from the digestive tract of the medicinal leech Hirudo verbana, using mucin as the primary carbon and energy source. These strains, designated M3(T), M4 and M6, were Gram-stain-negative, non-spore-forming and non-motile. Cells were elongated bacilli approximately 2.4 µm long and 0.6 µm wide. Growth only occurred anaerobically under mesophilic and neutral pH conditions. All three strains could utilize multiple simple and complex sugars as carbon sources, with glucose fermented to acid by-products. The DNA G+C contents of strains M3(T), M4 and M6 were 44.9, 44.8 and 44.8 mol%, respectively. The major cellular fatty acid of strain M3(T) was iso-C15?:?0. Phylogenetic analysis of full-length 16S rRNA gene sequences revealed that the three strains shared >99?% similarity with each other and represent a new lineage within the family Rikenellaceae of the order Bacteroidales, phylum Bacteroidetes. The most closely related bacteria to strain M3(T) based on 16S rRNA gene sequences were Rikenella microfusus DSM 15922(T) (87.3?% similarity) and Alistipes finegoldii AHN 2437(T) (87.4?%). On the basis of phenotypic, genotypic and physiological evidence, strains M3(T), M4 and M6 are proposed as representing a novel species of a new genus within the family Rikenellaceae, for which the name Mucinivorans hirudinis gen. nov., sp. nov. is proposed. The type strain of Mucinivorans hirudinis is M3(T) (?=?ATCC BAA-2553(T)?=?DSM 27344(T)). PMID:25563920

  5. Morphology and gene sequence of Levicoleps biwae n. gen., n. sp. (Ciliophora, Prostomatida), a proposed endemic from the ancient Lake Biwa, Japan.

    PubMed

    Foissner, Wilhelm; Kusuoka, Yasushi; Shimano, Satoshi

    2008-01-01

    Levicoleps biwae n. gen., n. sp. was discovered in organic mud on the shore of Lake Biwa, Japan. Its morphology and small subunit rRNA gene sequence were studied with standard methods. Further, we established a terminology for the colepid armour and selected four features for genus recognition: the number of armour tiers, the structure of the tier plates, the presence/absence of armour spines, and the number of adoral organelles (three or five). The Japanese colepid, a barrel-shaped ciliate with an average size of 75 x 45 microm, has six armour tiers and hirtus-type tier plates, but lacks armour spines, both in the environment and in laboratory culture. Thus, it is considered to represent a new genus. This rank is supported by the considerable genetic distance (7%) from the common Coleps hirtus. Although L. biwae looks quite similar to C. hirtus in vivo, it is very likely most closely related to Coleps amphacanthus, a species with conspicuous armour spines, as indicated by body size, the number of ciliary rows and, especially, the multiple caudal cilia. Lake Biwa is about four million years old and inhabited by many endemic organisms, ranging from algae to large fish. Thus, we suspect that L. biwae is restricted to Lake Biwa or, at least, to Asia. Based on literature data and the generic features established, we also propose the new genus Reticoleps for Coleps remanei Kahl, 1933, and resurrect the genus Pinacocoleps Diesing, 1865 to include Coleps incurvus Ehrenberg, 1833, Coleps pulcher Spiegel, 1926, Coleps tessalatus Kahl, 1930 and, probably, Baikalocoleps quadratus Obolkina, 1995a. Nine colepid genera are diagnosed and dichotomously keyed. PMID:18460156

  6. Rhizocola hellebori gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae containing 3,4-dihydroxydiaminopimelic acid in the cell-wall peptidoglycan.

    PubMed

    Matsumoto, Atsuko; Kawaguchi, Yoko; Nakashima, Takuji; Iwatsuki, Masato; ?mura, Satoshi; Takahashi, Y?ko

    2014-08-01

    An actinomycete strain, K12-0602(T), was isolated from the root of a Helleborus orientalis plant in Japan. The 16S rRNA gene sequence of strain K12-0602(T) showed that it had a close relationship with members of the family Micromonosporaceae and the 16S rRNA gene sequence similarity values between strain K12-0602(T) and type strains of type species of 27 genera belonging to the family Micromonosporaceae were below 96.2%. MK-9 (H4) and MK-9 (H6) were detected as major menaquinones, and galactose, xylose, mannose and ribose were present in the whole-cell hydrolysate. The acyl type of the peptidoglycan was glycolyl. Major fatty acids were iso-C(15?:?0), iso-C(16?:?0), C(17?:?1)?9c and anteiso-C(17?:?0). Phosphatidylethanolamine was detected as the phospholipid corresponding to phospholipid type II. The G+C content of the genomic DNA was 67 mol%. Analyses of the cell-wall peptidoglycan by TLC and LC/MS showed that it was composed of alanine, glycine, hydroxylglutamic acid and an unknown amino acid, which was subsequently determined to be 3,4-dihydroxydiaminopimelic acid using instrumental analyses, including NMR and mass spectrometry. On the basis of the phylogenetic analysis and chemotaxonomic characteristics, strain K12-0602(T) represents a novel species of a new genus in the family Micromonosporaceae, for which the name Rhizocola hellebori gen. nov., sp. nov. is proposed. The type strain of the type species is K12-0602(T) (?=?NBRC 109834(T)?=?DSM 45988(T)). This is the first report, to our knowledge, of 3,4-dihydroxydiaminopimelic acid being found as a diamino acid in bacterial cell-wall peptidoglycan. PMID:24893943

  7. Review of amphipods of the Melita group (Amphipoda: Melitidae) from the costal waters of Sakhalin Island (Far East of Russia). I. Genera Megamoera Bate, 1862 and Armatomelita gen. nov.

    PubMed

    Labay, Vjacheslav S

    2013-01-01

    A review of Melita group (fam. Melitidae) from the shelf of Sakhalin Island based on literature and own data is provided. Based on new material, four new species of the genus Megamoera are described: M. similidentata sp. nov. and M. striata sp. nov. from north-east shelf of Sakhalin Island; M falsomikulitschae sp. nov. and M. aequidentatum sp. nov. from Aniva Bay (southern Sakhalin). The new genus Armatomelita gen. nov. and new species A. tshayensis sp. nov. are described from Aniva Bay (southern Sakhalin). A key to the world species of the genus Megamoera is provided. Cladistic analysis of morphological relationships within the genus Megamoera is implemented. PMID:26106716

  8. Cultivation and characterization of the gut symbionts of honey bees and bumble bees: description of Snodgrassella alvi gen. nov., sp. nov., a member of the family Neisseriaceae of the Betaproteobacteria, and Gilliamella apicola gen. nov., sp. nov., a member of Orbaceae fam. nov., Orbales ord. nov., a sister taxon to the order 'Enterobacteriales' of the Gammaproteobacteria.

    PubMed

    Kwong, Waldan K; Moran, Nancy A

    2013-06-01

    Gut-associated bacteria were isolated in axenic culture from the honey bee Apis mellifera and the bumble bees Bombus bimaculatus and B. vagans and are here placed in the novel genera and species Snodgrassella alvi gen. nov., sp. nov. and Gilliamella apicola gen. nov., sp. nov. Two strains from A. mellifera were characterized and are proposed as the type strains of Snodgrassella alvi (type strain wkB2(T) =NCIMB 14803(T) =ATCC BAA-2449(T) =NRRL B-59751(T)) and Gilliamella apicola (type strain wkB1(T) =NCIMB 14804(T) =ATCC BAA-2448(T)), representing, respectively, phylotypes referred to as 'Betaproteobacteria' and 'Gammaproteobacteria-1'/'Gamma-1' in earlier publications. These strains grew optimally under microaerophilic conditions, and did not grow readily under a normal atmosphere. The predominant fatty acids in both strains were palmitic acid (C16:0) and cis-vaccenic acid (C18:1?7c and/or C18:1?6c), and both strains had ubiquinone-8 as their major respiratory quinone. The DNA G+C contents were 41.3 and 33.6 mol% for wkB2(T) and wkB1(T), respectively. The Snodgrassella alvi strains from honey bees and bumble bees formed a novel clade within the family Neisseriaceae of the Betaproteobacteria, showing about 94% 16S rRNA gene sequence identity to their closest relatives, species of Stenoxybacter, Alysiella and Kingella. The Gilliamella apicola strains showed the highest 16S rRNA gene sequence identity to Orbus hercynius CN3(T) (93.9%) and several sequences from uncultured insect-associated bacteria. Phylogenetic reconstruction using conserved, single-copy amino acid sequences showed Gilliamella apicola as sister to the order 'Enterobacteriales' of the Gammaproteobacteria. Given its large sequence divergence from and basal position to the well-established order 'Enterobacteriales', we propose to place the clade encompassing Gilliamella apicola and O. hercynius in a new family and order, Orbaceae fam. nov. and Orbales ord. nov. PMID:23041637

  9. Granulinema gen. n. a new dracunculoid genus with two new species (G. carcharhini sp. n. and G. simile sp. n.) from the bull shark, Carcharhinus leucas (Valenciennes), from Louisiana, USA.

    PubMed

    Moravec, F; Little, M D

    1988-01-01

    Two new species of dracunculoid nematodes, G. carcharhini sp. n. and G. simile sp. n., representing a new genus Granulinema gen. n. (Dracunculoidea: Micropleuridae) are described from the bull shark, Carcharhinus leucas, from Louisiana (Lake Borgne), USA; the site of their localization in the host is unknown (probably abdominal cavity). The nematodes of both species were found in tissue juice and only males, juvenile females and body fragments of more advanced but nongravid females were obtained. Granulinema gen. n. differs from Micropleura, the only other genus in the family Micropleuridae, mainly by the presence of marked, dark excretory corpuscles in lateral excretory canals, pointed tail in females, greater number (6) of postanal pairs of caudal papillae in males, and by the presence of conspicuous transverse cuticular ornamentations on the body surface of mature females. The two new species can be easily distinguished from each other by the length of their spicules (0.78-0.90 mm in G. carcharhini sp. n. and 0.20-0.36 mm in G. simile sp. n.); moreover, there are two pairs of preanal papillae in the male of G. carcharhini sp. n., while there are three pairs in G. simile sp. n. PMID:3169642

  10. Gregarines infecting Ischnura spp. in Texas, U.S.A., including description of Septemlaterospora rasberryi n. gen. n. sp. (Apicomplexa: Actinocephalidae: Acanthosporinae) and revision of Steganorhynchus dunwoodyi (Apicomplexa: Actinocephalidae: Menosporinae).

    PubMed

    Cook, Tamara J; Smith-Herron, Autumn J

    2014-02-01

    Septemlaterospora rasberryi n. gen. n. sp. (Apicomplexa: Eugregarinida: Actinocephalidae: Acanthosporinae) is described from adults of Ischnura ramburii (Odonata: Zygoptera: Coenagrionidae). Septemlaterospora n. gen is distinguished by the form of the oocysts: terminally truncated heptagonal bipyramids bearing 7 equatorial spines, 1 at each equatorial vertex, 7 terminal spines obliquely inserted at each pole, 1 at each vertex created by polar truncation; 21 spines total. The holdfast is compound, comprising a terminal epimerite and intercalating diamerite; epimerite is a thick disk or linearly crateriform sucker; diamerite is short (less than half of the total holdfast length) and very broadly obdeltoid. Association occurs immediately before syzygy and is cephalolateral and biassociative. Gametocysts are spherical with a conspicuous hyaline coat. Lacking conspicuous sporoducts, they dehisce by simple rupture. Steganorhynchus dunwoodyi is redescribed utilizing a new complete taxonomic data set, consisting of a larger set of metric characters and based on uniformly prepared, permanent specimens. New host and geographic records are reported for Calyxocephalus karyopera, Domadracunculus janovyi, Nubenocephalus secundus, and Steganorhynchus dunwoodyi, and the type host of D. janovyi is amended. PMID:23984837

  11. Tomaculocystis corpulenta n. gen., n. sp. (Apicomplexa: Eugregarinorida) parasitizing the little yellow cockroach, Cariblatta lutea (Blattodea: Ectobiidae), in Alabama and Florida with recognition of Tomaculocystis cylindrosa n. comb. and Tomaculocystis mukundai n. comb. parasitizing ectobiid cockroaches in India.

    PubMed

    Clopton, Richard E

    2015-02-01

    Tomaculocystis corpulenta n. gen., n. sp. (Apicomplexa: Eugregarinorida: Septatorina: Gregarinidae) is described from populations of the little yellow cockroach, Cariblatta lutea (Blattodea: Ectobiidae), established in laboratory culture from samples collected in Alabama and Florida. Tomaculocystis n. gen. are differentiated from other members of Gregarina by a markedly elliptoid gametocyst inside a persistent, lomentiform hyaline epicyst; developmental organization and growth of the spore tubes from gametocyst surface tumidi; and dehiscence by extrusion of non-chain forming oocysts through spore tubes that barely extend beyond the epicyst wall. Gregarina cylindrosa, Gregarina discocephala, and Gregarina mukundai are recognized as members of Tomaculocystis, and G. cylindrosa is recognized as the senior synonym of G. discocephala. Thus, Tomaculocystis cylindrosa n. comb. and Tomaculocystis mukundai n. comb. are formed. Species of Tomaculocystis are distinguished based on gamont deutomerite and oocyst shape and size. The oocysts of T. corpulenta are broadly dolioform, lack 4 polar knobs, and possess distinct, unique polar plates. Oocysts of all other known species in the genus are more oblong in shape, possess 4 polar knobs, and lack the distinct polar plates observed in the oocysts of T. corpulenta. Host utilization and geographic distribution among gregarine genera parasitizing the cockroach family Ectobiidae reveal a pattern of host-parasite specificity linking gregarine genera with ectobiidid subfamilies. Overall patterns suggest a hypothesis of European endemicy for Gamocystis, but hypotheses for the origin and radiation of Tomaculocystis or species of Gregarina infecting cockroaches are confounded by the cosmopolitan spread of pest cockroach species among humans. PMID:25153145

  12. Simulating land-use changes and stormwater-detention basins and evaluating their effect on peak streamflows and stream-water quality in Irondequoit Creek basin, New York : a user's manual for HSPF and GenScn

    USGS Publications Warehouse

    Coon, William F.

    2003-01-01

    A computer model of hydrologic and water-quality processes of the Irondequoit Creek basin in Monroe and Ontario Counties, N.Y., was developed during 2000-02 to enable water-resources managers to simulate the effects of future development and stormwater-detention basins on peak flows and water quality of Irondequoit Creek and its tributaries. The model was developed with the program Hydrological Simulation Program-Fortran (HSPF) such that proposed or hypothetical land-use changes and instream stormwater-detention basins could be simulated, and their effects on peak flows and loads of total suspended solids, total phosphorus, ammonia-plus-organic nitrogen, and nitrate-plus-nitrite nitrogen could be analyzed, through an interactive computer program known as Generation and Analysis of Model Simulation Scenarios for Watersheds (GenScn). This report is a user's manual written to guide the Irondequoit Creek Watershed Collaborative in (1) the creation of land-use and flow-detention scenarios for simulation by the HSPF model, and (2) the use of GenScn to analyze the results of these simulations. These analyses can, in turn, aid the group in making basin-wide water-resources-management decisions.

  13. Zwicknia gen. n., a new genus for the Capnia bifrons species group, with descriptions of three new species based on morphology, drumming signals and molecular genetics, and a synopsis of the West Palaearctic and Nearctic genera of Capniidae (Plecoptera).

    PubMed

    Murányi, Dávid; Gamboa, Maribet; Orci, Kirill Márk

    2014-01-01

    Zwicknia Murányi, gen. n. is erected for the Capnia bifrons species group sensu Zhiltzova, 2001 with the description of three new species based on morphology, mating call, and the mitochondrial DNA marker cytochrome c oxidase I: Z. acuta Murányi & Orci, sp. n., Z. kovacsi Murányi & Gamboa, sp. n. and Z. rupprechti Murányi, Orci & Gamboa, sp. n.. Zwicknia bifrons (Newman, 1838) comb. n. is selected as the type species and redescribed. The other three species placed into Zwicknia, gen. n., Z. sevanica (Zhiltzova, 1964) comb. n., Z. tuberculata (Zhiltzova, 1964) comb. n., and Z. turkestanica (Kimmins, 1950) comb. n. are redescribed based only on morphological characters. Comparative morphological studies and newly discovered characters of the genitalia has allowed for the first time a synopsis of the adults of the West Palaearctic and Nearctic genera of Capniidae. Arsapnia Banks, 1897 (type species: A. decepta Banks, 1897 comb. rev.) is removed from synonymy with Capnia Pictet, 1841 with new combinations, Arsapnia arapahoe (Nelson & Kondratieff, 1988) comb. n., A. coyote (Nelson & Baumann, 1987) comb. n., A. pileata (Jewett, 1966) comb. n., A. sequoia (Nelson & Baumann, 1987) comb. n., A. teresa (Claassen, 1924) comb. n., A. tumida (Claassen, 1924) comb. n., and A. utahensis (Gaufin & Jewett, 1962) comb. n. A new sensu stricto diagnosis of Capnia is proposed with comments on the taxa retained in Capnia sensu lato. PMID:24943267

  14. Use of Fe(III) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of Geothermobacterium ferrireducens gen. nov., sp. nov.

    PubMed

    Kashefi, Kazem; Holmes, Dawn E; Reysenbach, Anna-Louise; Lovley, Derek R

    2002-04-01

    It has recently been recognized that the ability to use Fe(III) as a terminal electron acceptor is a highly conserved characteristic in hyperthermophilic microorganisms. This suggests that it may be possible to recover as-yet-uncultured hyperthermophiles in pure culture if Fe(III) is used as an electron acceptor. As part of a study of the microbial diversity of the Obsidian Pool area in Yellowstone National Park, Wyo., hot sediment samples were used as the inoculum for enrichment cultures in media containing hydrogen as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. A pure culture was recovered on solidified, Fe(III) oxide medium. The isolate, designated FW-1a, is a hyperthermophilic anaerobe that grows exclusively by coupling hydrogen oxidation to the reduction of poorly crystalline Fe(III) oxide. Organic carbon is not required for growth. Magnetite is the end product of Fe(III) oxide reduction under the culture conditions evaluated. The cells are rod shaped, about 0.5 microm by 1.0 to 1.2 microm, and motile and have a single flagellum. Strain FW-1a grows at circumneutral pH, at freshwater salinities, and at temperatures of between 65 and 100 degrees C with an optimum of 85 to 90 degrees C. To our knowledge this is the highest temperature optimum of any organism in the Bacteria. Analysis of the 16S ribosomal DNA (rDNA) sequence of strain FW-1a places it within the Bacteria, most closely related to abundant but uncultured microorganisms whose 16S rDNA sequences have been previously recovered from Obsidian Pool and a terrestrial hot spring in Iceland. While previous studies inferred that the uncultured microorganisms with these 16S rDNA sequences were sulfate-reducing organisms, the physiology of the strain FW-1a, which does not reduce sulfate, indicates that these organisms are just as likely to be Fe(III) reducers. These results further demonstrate that Fe(III) may be helpful for recovering as-yet-uncultured microorganisms from hydrothermal environments and illustrate that caution must be used in inferring the physiological characteristics of at least some thermophilic microorganisms solely from 16S rDNA sequences. Based on both its 16S rDNA sequence and physiological characteristics, strain FW-1a represents a new genus among the Bacteria. The name Geothermobacterium ferrireducens gen. nov., sp. nov., is proposed (ATCC BAA-426). PMID:11916691

  15. Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs.

    PubMed

    Pankratov, Timofey A; Dedysh, Svetlana N

    2010-12-01

    Five strains of strictly aerobic, heterotrophic bacteria that form pink-red colonies and are capable of hydrolysing pectin, xylan, laminarin, lichenan and starch were isolated from acidic Sphagnum peat bogs and were designated OB1010(T), LCBR1, TPB6011(T), TPB6028(T) and TPO1014(T). Cells of these isolates were Gram-negative, non-motile rods that produced an amorphous extracellular polysaccharide-like substance. Old cultures contained spherical bodies of varying sizes, which represent starvation forms. Cells of all five strains were acidophilic and psychrotolerant, capable of growth at pH 3.0-7.5 (optimum pH 3.8-4.5) and at 2-33°C (optimum 15-22°C). The major fatty acids were iso-C(15?:?0), C(16?:?0) and summed feature 3 (C(16?:?1)?7c and/or iso-C(15?:?0) 2-OH). The major menaquinone detected was MK-8. The pigments were carotenoids. The genomic DNA G+C contents were 57.3-59.3 mol%. The five isolates were found to be members of subdivision 1 of the phylum Acidobacteria and displayed 95.3-98.9?% 16S rRNA gene sequence similarity to each other. The closest described relatives to strains OB1010(T), LCBR1, TPB6011(T), TPB6028(T), and TPO1014(T) were members of the genera Terriglobus (94.6-95.8?% 16S rRNA gene sequence similarity) and Edaphobacter (94.2-95.4?%). Based on differences in cell morphology, phenotypic characteristics and hydrolytic capabilities, we propose a novel genus, Granulicella gen. nov., containing four novel species, Granulicella paludicola sp. nov. with type strain OB1010(T) (=DSM 22464(T) =LMG 25275(T)) and strain LCBR1, Granulicella pectinivorans sp. nov. with type strain TPB6011(T) (=VKM B-2509(T) =DSM 21001(T)), Granulicella rosea sp. nov. with type strain TPO1014(T) (=DSM 18704(T) =ATCC BAA-1396(T)) and Granulicella aggregans sp. nov. with type strain TPB6028(T) (=LMG 25274(T) =VKM B-2571(T)). PMID:20118293

  16. Desulfoprunum benzoelyticum gen. nov., sp. nov., a Gram-stain-negative, benzoate-degrading, sulfate-reducing bacterium isolated from a wastewater treatment plant.

    PubMed

    Junghare, Madan; Schink, Bernhard

    2015-01-01

    A strictly anaerobic, mesophilic, sulfate-reducing bacterium, strain KoBa311(T), isolated from the wastewater treatment plant at Konstanz, Germany, was characterized phenotypically and phylogenetically. Cells were Gram-stain-negative, non-motile, oval to short rods, 3-5 µm long and 0.8-1.0 µm wide with rounded ends, dividing by binary fission and occurring singly or in pairs. The strain grew optimally in freshwater medium and the optimum temperature was 30 °C. Strain KoBa311(T) showed optimum growth at pH 7.3-7.6. Organic electron donors were oxidized completely to carbon dioxide concomitant with sulfate reduction to sulfide. At excess substrate supply, substrates were oxidized incompletely and acetate (mainly) and/or propionate accumulated. The strain utilized short-chain fatty acids, alcohols (except methanol) and benzoate. Sulfate and DMSO were used as terminal electron acceptors for growth. The genomic DNA G+C content was 52.3 mol% and the respiratory quinone was menaquinone MK-5 (V-H2). The major fatty acids were C16:0, C16:1?7c/?6c and C18:1?7c. Phylogenetic analysis based on 16S rRNA gene sequences placed strain KoBa311(T) within the family Desulfobulbaceae in the class Deltaproteobacteria. Its closest related bacterial species on the basis of the distance matrix were Desulfobacterium catecholicum DSM 3882(T) (93.0% similarity), Desulfocapsa thiozymogenes (93.1%), Desulforhopalus singaporensis (92.9%), Desulfopila aestuarii (92.4%), Desulfopila inferna JS_SRB250Lac(T) (92.3%) and Desulfofustis glycolicus (92.3%). On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain KoBa311(T) was distinct from any related type species. Therefore, strain KoBa311(T) is considered to represent a novel species of a new genus, for which the name Desulfoprunum benzoelyticum gen. nov., sp. nov. is proposed. The type strain of Desulfoprunum benzoelyticum is KoBa311(T) (?=DSM 28570(T)?=KCTC 15441(T)). PMID:25278560

  17. Clinical Evaluation of the Enhanced Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test for Rapid Diagnosis of Tuberculosis in Prison Inmates†

    PubMed Central

    Bergmann, John S.; Yuoh, Gbo; Fish, Geoffrey; Woods, Gail L.

    1999-01-01

    The reliability of the enhanced Amplified Mycobacterium Tuberculosis Direct Test (E-MTD; Gen-Probe, Inc., San Diego, Calif.) for rapid diagnosis of pulmonary tuberculosis (TB) was evaluated by testing 1,004 respiratory specimens from 489 Texas prison inmates. Results were compared to those of mycobacterial culture (BACTEC TB 460 and Middlebrook 7H11 biplates), smear for acid-fast bacilli (AFB; auramine O), and clinical course. After chart review, three patients (nine specimens) who were on antituberculosis therapy before the study began were excluded from final analysis. Of the remaining 995 specimens, 21 were AFB smear positive: 13 grew Mycobacterium tuberculosis complex (MTBC), 6 grew nontuberculous mycobacteria, and 2 (from two patients diagnosed with TB and started on therapy after the study began) were culture negative. Twenty-eight specimens (20 patients) were positive for MTBC by culture and E-MTD. Seven specimens (seven patients) were positive by culture alone; three were from patients who had other E-MTD-positive specimens, two were false-positive cultures, and two were false-negative E-MTD results. Eight specimens were positive by E-MTD only; four specimens (four patients) were false-positive E-MTD results, and four specimens were from two patients with earlier E-MTD-positive specimens that grew MTBC. Thus, there were 22 patients with TB (10 smear positive and 12 smear negative). The sensitivity and specificity of the AFB smear for diagnosis of TB, by patient, were 45.5 and 98.9%, respectively. After resolving discrepancies, these same values for E-MTD were 90.9 and 99.1% overall, 100 and 100% for the smear-positive patients, and 83.3 and 99.1% for the smear-negative patients. Excluding the one smear-negative patient whose E-MTD-negative, MTBC culture-positive specimen contained inhibitory substances, the sensitivity of E-MTD was 95.2% overall and 90.9% in smear-negative patients. The specificity and positive predictive value of E-MTD can be improved, without altering other performance characteristics, by modifying the equivocal zone recommended by the manufacturer. These data suggest that E-MTD is a reliable method for rapid diagnosis of pulmonary TB, irrespective of the AFB smear result. Guidelines for the most appropriate use of E-MTD with smear-negative patients are needed. PMID:10203498

  18. Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil.

    PubMed

    Huber, Katharina J; Wüst, Pia K; Rohde, Manfred; Overmann, Jörg; Foesel, Bärbel U

    2014-06-01

    Acidobacteria constitute an abundant fraction of the soil microbial community and are currently divided into 26 subdivisions. Most cultivated members of the Acidobacteria are affiliated with subdivision 1, while only a few representatives of subdivisions 3, 4, 8, 10 and 23 have been isolated and described so far. Two novel isolates of subdivision 4 of the Acidobacteria were isolated from subtropical savannah soils and are characterized in the present work. Cells of strains A22_HD_4H(T) and Ac_23_E3(T) were immotile rods that divided by binary fission. Colonies were pink and white, respectively. The novel strains A22_HD_4H(T) and Ac_23_E3(T) were aerobic mesophiles with a broad range of tolerance towards pH (4.0-9.5 and 3.5-10.0, respectively) and temperature (15-44 and 12-47 °C, respectively). Both showed chemo-organoheterotrophic growth on some sugars, the amino sugar N-acetylgalactosamine, a few amino acids, organic acids and various complex protein substrates. Major fatty acids of A22_HD_4H(T) and Ac_23_E3(T) were iso-C(15?:?0), summed feature 1 (C(13?:?0) 3-OH/iso-C(15?:?1) H), summed feature 3 (C(16?:?1)?7c/C(16?:?1)?6c) and anteiso-C(17?:?0). The major quinone was MK-8; in addition, MK-7 occurred in small amounts. The DNA G+C contents of A22_HD_4H(T) and Ac_23_E3(T) were 53.2 and 52.6 mol%, respectively. The closest described relative was Blastocatella fastidiosa A2-16(T), with 16S rRNA gene sequence identity of 93.2 and 93.3%, respectively. Strains A22_HD_4H(T) and Ac_23_E3(T) displayed 16S rRNA gene sequence similarity of 97.4% to each other. On the basis of the low DNA-DNA hybridization value, the two isolates represent different species. Based on morphological, physiological and molecular characteristics, the new genus Aridibacter gen. nov. is proposed, with two novel species, the type species Aridibacter famidurans sp. nov. (type strain A22_HD_4H(T)?=?DSM 26555(T)?=?LMG 27985(T)) and a second species, Aridibacter kavangonensis sp. nov. (type strain Ac_23_E3(T)?=?DSM 26558(T)?=?LMG 27597(T)). PMID:24573163

  19. Phaeocystidibacter luteus gen. nov., sp. nov., a member of the family Cryomorphaceae isolated from the marine alga Phaeocystis globosa, and emended description of Owenweeksia hongkongensis.

    PubMed

    Zhou, Yanyan; Su, Jianqiang; Lai, Qiliang; Li, Xinyi; Yang, Xiaoru; Dong, Peiyan; Zheng, Tianling

    2013-03-01

    A taxonomic study was carried out on strain PG2S01(T), isolated from a culture of Phaeocystis globosa, a haemolytic, toxin-producing, harmful marine alga. Cells of strain PG2S01(T) were Gram-negative, strictly aerobic, non-motile, non-fermentative, orange-pigmented, moderately halophilic rods. Growth was observed in the presence of 0.25-7.5?% NaCl and at 10-40 °C. The dominant fatty acids were iso-C15?:?0, summed feature 3 (C16?:?1?7c and/or C16?:?1?6c), iso-C17?:?0 3-OH, iso-C16?:?0 3-OH, iso-C15?:?1 G and iso-C15?:?0 3-OH. The major polar lipids were phosphatidylethanolamine and several unidentified aminolipids, phospholipids and other lipids. The G+C content of the chromosomal DNA was 44.6 mol%. 16S rRNA gene sequence comparison showed that strain PG2S01(T) was most closely related to Owenweeksia hongkongensis UST20020801(T) (88.9?% 16S rRNA gene sequence similarity); levels of similarity between strain PG2S01(T) and the type strains of recognized representatives of genera in the family Cryomorphaceae were <88?%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PG2S01(T) formed a distinct evolutionary lineage within the family Cryomorphaceae. Strain PG2S01(T) was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of phenotypic data and phylogenetic inference, strain PG2S01(T) represents a novel species in a new genus in the family Cryomorphaceae, for which the name Phaeocystidibacter luteus gen. nov., sp. nov. is proposed. The type strain of the type species is PG2S01(T) (?=?CCTCC AB 209288(T) ?=?LMG 25704(T) ?=?MCCC 1F01079(T)). An emended description of O. hongkongensis Lau et al. 2005 is also proposed. PMID:22753526

  20. Desulfocarbo indianensis gen. nov., sp. nov., a benzoate-oxidizing, sulfate-reducing bacterium isolated from water extracted from a coal bed.

    PubMed

    An, Thuy T; Picardal, Flynn W

    2014-08-01

    A novel, strictly anaerobic, sulfate-reducing bacterium, designated strain SCBM(T), was isolated from water extracted from a coal bed in Indiana, USA. The isolate was characterized by a polyphasic taxonomic approach that included phenotypic and genotypic characterizations. Cells of strain SCBM(T) were vibrio-shaped, polarly flagellated, Gram-negative, motile, oxidase-negative and weakly catalase-positive. Growth of strain SCBM(T) was observed at NaCl concentrations ranging from 0 to 300 mM. However, no growth was observed when 1 M or more NaCl was present. Growth was observed at 16-37 °C, with optimal growth at 30 °C. The optimum pH for growth was 7, although growth was observed from pH 6.5 to 8. The doubling time under optimal growth conditions (30 °C, pH 7, 2.5 mM benzoate, 14 mM sulfate) was 2.7 days. Bicarbonate, HEPES, PIPES and MES were effective buffers for growth of strain SCBM(T), but citrate inhibited growth. When sulfate was provided as the electron acceptor, strain SCBM(T) grew autotrophically with hydrogen as the electron donor and heterotrophically on benzoate, formate, acetate, pyruvate, butyrate, fumarate, succinate and palmitate. None of the substrates tested supported fermentative growth. Thiosulfate and sulfate were used as electron acceptors coupled to benzoate oxidation, but sulfite, elemental sulfur, DMSO, anthraquinone 2,6-disulfonate, nitrate, nitrite, ferric citrate, hydrous iron oxide and oxygen were not. The G+C content of genomic DNA was 62.5?mol%. The major cellular fatty acids were anteiso-C(15?:?0) and C(18?:?1)?7c. Phylogenetic analysis based on 16S rRNA gene sequencing placed strain SCBM(T) into a distinct lineage within the class Deltaproteobacteria. The closest, cultivated phylogenetic relative of strain SCBM(T) was Desulfarculus baarsii DSM 2075(T), with only 91.7% 16S rRNA gene sequence identity. On the basis of phenotypic and genotypic analyses, strain SCBM(T) represents a novel genus and species of sulfate-reducing bacteria, for which the name Desulfocarbo indianensis gen. nov., sp. nov. is proposed. The type strain of Desulfocarbo indianensis is SCBM(T) (?=?DSM 28127(T)?=?JCM 19826(T)). Desulfocarbo is the second genus of the order Desulfarculales. PMID:24876241

  1. Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat

    PubMed Central

    2015-01-01

    During a study of the anaerobic microbial community of a lithifying hypersaline microbial mat of Lake 21 on the Kiritimati atoll (Kiribati Republic, Central Pacific) strain L21-RPul-D2T was isolated. The closest phylogenetic neighbor was Spirochaeta africana Z-7692T that shared a 16S rRNA gene sequence identity value of 90% with the novel strain and thus was only distantly related. A comprehensive polyphasic study including determination of the complete genome sequence was initiated to characterize the novel isolate. Cells of strain L21-RPul-D2T had a size of 0.2 – 0.25?×?8–9 ?m, were helical, motile, stained Gram-negative and produced an orange carotenoid-like pigment. Optimal conditions for growth were 35°C, a salinity of 50 g/l NaCl and a pH around 7.0. Preferred substrates for growth were carbohydrates and a few carboxylic acids. The novel strain had an obligate fermentative metabolism and produced ethanol, acetate, lactate, hydrogen and carbon dioxide during growth on glucose. Strain L21-RPul-D2T was aerotolerant, but oxygen did not stimulate growth. Major cellular fatty acids were C14:0, iso-C15:0, C16:0 and C18:0. The major polar lipids were an unidentified aminolipid, phosphatidylglycerol, an unidentified phospholipid and two unidentified glycolipids. Whole-cell hydrolysates contained L-ornithine as diagnostic diamino acid of the cell wall peptidoglycan. The complete genome sequence was determined and annotated. The genome comprised one circular chromosome with a size of 3.78 Mbp that contained 3450 protein-coding genes and 50 RNA genes, including 2 operons of ribosomal RNA genes. The DNA G?+?C content was determined from the genome sequence as 51.9 mol%. There were no predicted genes encoding cytochromes or enzymes responsible for the biosynthesis of respiratory lipoquinones. Based on significant differences to the uncultured type species of the genus Spirochaeta, S. plicatilis, as well as to any other phylogenetically related cultured species it is suggested to place strain L21-RPul-D2T (=DSM 27196T?=?JCM 18663T) in a novel species and genus, for which the name Salinispira pacifica gen. nov., sp. nov. is proposed.

  2. Gene panels to help identify subgroups at high and low risk of CHD among those randomized to antihypertensive treatment: The GenHAT Study

    PubMed Central

    Lynch, Amy I.; Eckfeldt, John H.; Davis, Barry R.; Ford, Charles E.; Boerwinkle, Eric; Leiendecker-Foster, Catherine; Arnett, Donna K.

    2012-01-01

    Objective To identify panels of genetic variants that predict treatment-related coronary heart disease (CHD) outcomes in hypertensive patients on one of four different classes of initial antihypertensive treatment. The goal was to identify subgroups of people based on their genetic profile who benefit most from a particular treatment. Methods Candidate genetic variants (n=78) were genotyped in 39,114 participants from GenHAT, ancillary to ALLHAT. ALLHAT randomized hypertensive participants (>=55 years) to one of four treatments (amlodipine, chlorthalidone, doxazosin, lisinopril). The primary outcome was fatal CHD or non-fatal MI (mean follow-up=4.9 years). A pharmacogenetic panel was derived within each of the four treatment groups. ROC curves estimated the discrimination rate between those with and without a CHD event, based on the addition of the genetic panel risk score. Results For each treatment group, we identified a panel of genetic variants that collectively improved prediction of CHD to a small but statistically significant extent. Chlorthalidone (A): NOS3, rs3918226; SELE, rs5361; ICAM1, rs1799969; AGT, rs5051; GNAS, rs7121; ROC comparison p=.004; Amlodipine (B): MMP1, rs1799750; F5, rs6025; NPPA, rs5065; PDE4D, rs6450512; MMP9, rs2274756; ROC comparison p=.006; Lisinopril (C): AGT, rs5051; PON1, rs705379; MMP12, rs652438; F12, rs1801020; GP1BA, rs6065; PDE4D, rs27653; ROC comparison p=.01; Doxazosin (D): F2, rs1799963; PAI1, rs1799768; MMP7, rs11568818; AGT, rs5051; ACE, rs4343; MMP2, rs243865; ROC comparison p=.007. Each panel was tested for a pharmacogenetic effect; panels A, B and D showed such evidence (p=.009, .006, and .001 respectively), panel C did not (p=.09). Conclusion Because each panel was associated with CHD in a specific treatment group but not the others, this research provides evidence that it may be possible to use gene panel scores as a tool to better assess antihypertensive treatment choices to reduce CHD risk in hypertensive individuals. PMID:22388798

  3. Allelic frequencies for SNP variants in the gene Nramp1 in bovine infected with Brucella abortus or classified by resistance to the pathogen Frecuencias alélicas para variantes SNP en el gen Nramp1 en bovinos infectados con Brucella abortus o clasificados por resistencia al patógeno

    Microsoft Academic Search

    Esperanza Rueda

    The natural resistance to brucellosis in cattle has been associated to genetic factors mainly to some single nucleotide polymorphism (SNP), located within Nramp1 gen. The current research has studied the effect of nucleotide variants to be found in coding regions and other one located in 3 non translated region of Nramp1 gene, on the animal classification as resistant or susceptible,

  4. NextGen protein design

    PubMed Central

    Regan, Lynne

    2014-01-01

    Protein engineering is at an exciting stage because designed protein–protein interactions are being used in many applications. For instance, three designed proteins are now in clinical trials. Although there have been many successes over the last decade, protein engineering still faces numerous challenges. Often, designs do not work as anticipated and they still require substantial redesign. The present review focuses on the successes, the challenges and the limitations of rational protein design today. PMID:24059497

  5. tostandoutfromthecrowd? NextGen Immunology

    E-print Network

    Shapiro, Ehud

    to Immunology research Microbiome and host interactions in health and disease Immune cell development (thymus widely used therapeutics for diseases such as Multiple Sclerosis, Inflammatory Bowel Disease, Bone Marrow and medicine, including immunogenomics, microbiome study, host pathogen interactions, cancer immunology

  6. Alteribacillus bidgolensis gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Bacillus persepolensis as Alteribacillus persepolensis comb. nov.

    PubMed

    Didari, Maryam; Amoozegar, Mohammad Ali; Bagheri, Maryam; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2012-11-01

    A novel Gram-stain-positive, moderately halophilic bacterium, designated strain P4B(T), was isolated from water of the hypersaline Aran-Bidgol lake in Iran and characterized taxonomically by using a polyphasic approach. Cells of strain P4B(T) were non-motile rods producing ellipsoidal endospores at a central position in non-swollen sporangia. Strain P4B(T) was strictly aerobic and catalase- and oxidase-positive. It was able to grow at NaCl concentrations of 0.5-12.5% (w/v), with optimum growth occurring at 5-7.5% (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain P4B(T) was shown to belong to the phylum Firmicutes and shared highest similarity with Bacillus persepolensis HS136(T) (97.1%) and Bacillus salarius BH169(T) (95.1%). However, it shared only 91.3% 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10(T), indicating that strain P4B(T) might not be a member of the genus Bacillus. The DNA G+C content of this new isolate was 38.9 mol%. DNA-DNA hybridization experiments revealed a low level of relatedness between strain P4B(T) and B. persepolensis HS136(T) (6%). The major cellular fatty acids of strain P4B(T) were iso-C(15:0) and anteiso-C(15:0), as for B. persepolensis HS136(T) but in contrast to B. salarius DSM 16461(T) and B. subtilis subsp. subtilis DSM 10(T). Its polar lipid pattern consisted of phosphatidylglycerol, an aminoglycolipid and an unknown phospholipid. This polar lipid profile was similar to that obtained for B. persepolensis DSM 21632(T) but different from those of B. salarius DSM 16461(T) and B. subtilis subsp. subtilis DSM 10(T). The isoprenoid quinones were MK-7 (88%) and MK-8 (2%). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features indicate placement of strain P4B(T) within the Firmicutes, closely related to B. persepolensis but with features clearly distinct from those of the genus Bacillus and other related genera. On the basis of these data, strain P4B(T) is considered to represent a novel species of a new genus, for which the name Alteribacillus bidgolensis gen. nov., sp. nov. is proposed. The type strain of Alteribacillus bidgolensis is P4B(T) (=CCM 7963(T)=CECT 7998(T)=DSM 25260(T)=IBRC-M 10614(T)=KCTC 13821(T)). It is also suggested to transfer B. persepolensis to this new genus, as Alteribacillus persepolensis comb. nov. The type strain of Alteribacillus persepolensis is HS136(T) (=CCM 7595(T)=DSM 21632(T)=JCM 15720(T)=LMG 25222(T)). PMID:22228653

  7. Proposal to replace the illegitimate genus name Bryantella Wolin et al. 2004VP with the genus name Marvinbryantia gen. nov. and to replace the illegitimate combination Bryantella formatexigens Wolin et al. 2004VP with Marvinbryantia formatexigens comb. nov.

    PubMed

    Wolin, Meyer J; Miller, Terry L; Lawson, Paul A

    2008-03-01

    The prokaryote generic name Bryantella Wolin et al. 2004(VP) is illegitimate because it is a later homonym of Bryantella Chickering, 1946 (Animalia, Arthropoda, Arachnida, Araneae, Salticidae, Dendryphantinae, Dendryphantini) and a later homonym of Bryantella Britton, 1957 (Animalia, Arthropoda, Scarabaeoidea, Scarabaeidae, Melolonthinae) [Principle 2, Rule 51b(4) of the Bacteriological Code (1990 Revision)]. Bryantella represents a genus of jumping spiders within the family Salticidae and a genus of melolonthine scarab beetles within the family Scarabaeidae. Therefore, a new genus name, Marvinbryantia gen. nov., is proposed for this taxon. As a result, a new combination, Marvinbryantia formatexigens comb. nov., is required for the type species to replace the illegitimate combination Bryantella formatexigens Wolin et al. 2004(VP). PMID:18319487

  8. Reclassification of Leifsonia ginsengi (Qiu et al. 2007) as Herbiconiux ginsengi gen. nov., comb. nov. and description of Herbiconiux solani sp. nov., an actinobacterium associated with the phyllosphere of Solanum tuberosum L.

    PubMed

    Behrendt, Undine; Schumann, Peter; Hamada, Moriyuki; Suzuki, Ken-Ichiro; Spröer, Cathrin; Ulrich, Andreas

    2011-05-01

    In the context of studying the effects of transgenic fructan-producing potatoes on the community structure of phyllosphere bacteria, a group of strains closely related to the species Leifsonia ginsengi was isolated. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the new isolates and L. ginsengi DSM 19088(T) formed a lineage at the genus level and this finding was supported by chemotaxonomic characterization. The peptidoglycan type of the representative isolate, K134/01(T), and L. ginsengi DSM 19088(T) was B2?, with d- and l-diaminobutyric acid as the diagnostic diamino acid and glycine, alanine and threo-3-hydroxyglutamic acid. The almost-complete substitution of glutamic acid by threo-3-hydroxyglutamic acid supported the differentiation of the new strains from recognized species of the genus Leifsonia. Furthermore, the detection of substantial amounts of the fatty acid cyclohexyl-C(17 : 0) in the new isolates and L. ginsengi DSM 19088(T) was a prominent chemotaxonomic feature for a clear demarcation of these strains from all genera of the family Microbacteriaceae that display the B2? cell-wall type. Comparative phylogenetic and phenotypic analyses of the isolates and L. ginsengi DSM 19088(T) revealed the separate species status of the isolates. On the basis of these results, it is proposed that L. ginsengi should be classified as the type species of a novel genus, Herbiconiux gen. nov., with the name Herbiconiux ginsengi gen. nov., comb. nov. (type strain wged11(T)?=?CGMCC 4.3491(T)?=?JCM 13908(T)?=?DSM 19088(T)?=?NBRC 104580(T)). The phyllosphere isolates are assigned to a novel species, Herbiconiux solani sp. nov. (type strain K134/01(T)?=?DSM 19813(T)?=?LMG 24387(T)?=?NBRC 106740(T)). PMID:20511458

  9. Measurements of the neutron electric to magnetic form-factor ratio G(En) / G(Mn) via the H-2(polarized-e, e-prime,polarized-n)H-1 reaction to Q**2 = 1.45-(GeV/c)**2

    SciTech Connect

    Bradley Plaster; A.Yu. Semenov; A. Aghalaryan; Erick Crouse; Glen MacLachlan; Shigeyuki Tajima; William Tireman; Abdellah Ahmidouch; Brian Anderson; Hartmuth Arenhovel; Razmik Asaturyan; O. Baker; Alan Baldwin; David Barkhuff; Herbert Breuer; Roger Carlini; Michael Christy; Steve Churchwell; Leon Cole; Samuel Danagoulian; Donal Day; T. Eden; Mostafa Elaasar; Rolf Ent; Manouchehr Farkhondeh; Howard Fenker; John Finn; Liping Gan; Ashot Gasparian; Kenneth Garrow; Paul Gueye; Calvin Howell; Bitao Hu; Mark Jones; James Kelly; Cynthia Keppel; Mahbubul Khandaker; Wooyoung Kim; Stanley Kowalski; Allison Lung; David Mack; Richard Madey; D. Manley; Pete Markowitz; Joseph Mitchell; Hamlet Mkrtchyan; Allena Opper; Charles Perdrisat; Vina Punjabi; Brian Raue; Tilmann Reichelt; Joerg Reinhold; Julie Roche; Yoshinori Sato; Nikolai Savvinov; Irina Semenova; Wonick Seo; Neven Simicevic; Gregory Smith; Stepan Stepanyan; Vardan Tadevosyan; Liguang Tang; Shawn Taylor; Paul Ulmer; William Vulcan; John Watson; Steven Wells; Frank Wesselmann; Stephen Wood; Seunghoon Yang; Lulin Yuan; Wei-Ming Zhang; Hong Guo Zhu; Xiaofeng Zhu

    2006-02-01

    We report values for the neutron electric to magnetic form factor ratio, G{sub En}/G{sub Mn}, deduced from measurements of the neutron's recoil polarization in the quasielastic {sup 2}H({rvec e}, e{prime}{rvec n}) {sup 1}H reaction, at three Q{sup 2} values of 0.45, 1.13, and 1.45 (GeV/c){sup 2}. The data at Q{sup 2} = 1.13 and 1.45 (GeV/c){sup 2} are the first direct experimental measurements of GEn employing polarization degrees of freedom in the Q{sup 2} > 1 (GeV/c){sup 2} region and stand as the most precise determinations of GEn for all values of Q{sup 2}.

  10. Comparison of Biolog GEN III MicroStation semi-automated bacterial identification system with matrix-assisted laser desorption ionization-time of flight mass spectrometry and 16S ribosomal RNA gene sequencing for the identification of bacteria of veterinary interest.

    PubMed

    Wragg, P; Randall, L; Whatmore, A M

    2014-10-01

    Recent advances in phenotypic and chemotaxonomic methods have improved the ability of systems to resolve bacterial identities at the species level. Key to the effective use of these systems is the ability to draw upon databases which can be augmented with new data gleaned from atypical or novel isolates. In this study we compared the performance of the Biolog GEN III identification system (hereafter, GEN III) with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing in the identification of isolates of veterinary interest. The use of strains that had proven more difficult to identify by routine methods was designed to test the systems' abilities at the extremes of their performance range. Over an 18month period, 100 strains were analysed by all three methods. To highlight the importance of identification to species level, a weighted scoring system was devised to differentiate the capacity to identify at genus and species levels. The overall relative weighted scores were 0.869:0.781:0.769, achieved by 16S rRNA gene sequencing, GEN III and MALDI-TOF MS respectively, when compared to the 'gold standard'. Performance to the genus level was significantly better using 16S rRNA gene sequencing; however, performance to the species level was similar for all three systems. PMID:25014253

  11. Primary hyperoxaluria type 1 in the Canary Islands: A conformational disease due to I244T mutation in the P11L-containing alanine:glyoxylate aminotransferase

    PubMed Central

    Santana, A.; Salido, E.; Torres, A.; Shapiro, L. J.

    2003-01-01

    Primary hyperoxaluria type 1 (PH1) is an inborn error of metabolism resulting from a deficiency of alanine:glyoxylate aminotransferase (AGXT; EC 2.6.1.44). Most of the PH1 alleles detected in the Canary Islands carry the Ile-244 ? Thr (I244T) mutation in the AGXT gene, with 14 of 16 patients homozygous for this mutation. Four polymorphisms within AGXT and regional microsatellites also were shared in their haplotypes (AGXT*LTM), consistent with a founder effect. The consequences of these amino acid changes were investigated. Although I244T alone did not affect AGXT activity or subcellular localization, when present in the same protein molecule as Leu-11 ? Pro (L11P), it resulted in loss of enzymatic activity in soluble cell extracts. Like its normal counterpart, the AGXT*LTM protein was present in the peroxisomes but it was insoluble in detergent-free buffers. The polymorphism L11P behaved as an intragenic modifier of the I244T mutation, with the resulting protein undergoing stable interaction with molecular chaperones and aggregation. This aggregation was temperature-sensitive. AGXT*LTM expressed in Escherichia coli, as a GST-fusion protein, and in insect cells could be purified and retained enzymatic activity. Among various chemical chaperones tested in cell culture, betaine substantially improved the solubility of the mutant protein and the enzymatic activity in cell lysates. In summary, I244T, the second most common mutation responsible for PH1, is a protein conformational disease that may benefit from new therapies with pharmacological chaperones or small molecules to minimize protein aggregation. PMID:12777626

  12. Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes1[OPEN

    PubMed Central

    Law, MeiYee; Childs, Kevin L.; Campbell, Michael S.; Stein, Joshua C.; Olson, Andrew J.; Holt, Carson; Panchy, Nicholas; Lei, Jikai; Jiao, Dian; Andorf, Carson M.; Lawrence, Carolyn J.; Ware, Doreen; Shiu, Shin-Han; Sun, Yanni; Jiang, Ning; Yandell, Mark

    2015-01-01

    The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (Zea mays) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes. PMID:25384563

  13. Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum 'Acidobacteria'.

    PubMed

    Fukunaga, Yukiyo; Kurahashi, Midori; Yanagi, Kensuke; Yokota, Akira; Harayama, Shigeaki

    2008-11-01

    Strain FYK2218(T) was isolated from a specimen of the chiton Acanthopleura japonica, which had been collected from a beach on the Boso peninsula in Japan. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strain belonged to the phylum 'Acidobacteria'. The most closely related type strains to strain FYK2218(T) were Holophaga foetida TMBS4(T) (83.6 % 16S rRNA gene sequence similarity) and Geothrix fermentans H-5(T) (83.6 %) in subdivision 8 of the 'Acidobacteria'. Cells of FYK2218(T) were motile, rod-shaped, Gram-negative, mesophilic and strictly aerobic. The G+C content of the strain was 56.7 mol%. The strain had isoprenoid quinones MK-6 and MK-7 as major components. Major fatty acids of the strain were iso-C(15 : 0), iso-C(17 : 0), C(16 : 0) and C(20 : 5)omega3c (cis-5,8,11,14,17-eicosapentaenoic acid). From the taxonomic data obtained in this study, it is proposed that the new marine isolate be placed into a novel genus and species named Acanthopleuribacter pedis gen. nov., sp. nov. within the new family, order and class Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov. and Holophagae classis nov. The family Holophagaceae fam. nov. is also described. The type strain of Acanthopleuribacter pedis is FYK2218(T) (=NBRC 101209(T) =KCTC 12899(T)). PMID:18984699

  14. Thiogranum longum gen. nov., sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the family Ectothiorhodospiraceae isolated from a deep-sea hydrothermal field, and an emended description of the genus Thiohalomonas.

    PubMed

    Mori, Koji; Suzuki, Ken-ichiro; Yamaguchi, Kaoru; Urabe, Tetsuro; Hanada, Satoshi

    2015-01-01

    A novel, obligately chemolithoautotrophic, sulfur-oxidizing bacterial strain, designated strain gps52(T), was isolated from a rock sample collected near the hydrothermal vents of the Suiyo Seamount in the Pacific Ocean. The cells possessed a Gram-stain-negative-type cell wall and contained menaquinone-8(H4) and menaquinone-9(H4) as respiratory quinones, and C16?:?1?7c, C16?:?0 and C18?:?1?7c as major cellular fatty acids. Neither storage compounds nor extensive internal membranes were observed in the cells. Strain gps52(T) grew using carbon dioxide fixation and oxidation of inorganic sulfur compounds with oxygen as electron acceptor. Optimal growth was observed at 32 °C, pH 6.5 and with 3?% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain gps52(T) belongs to the family Ectothiorhodospiraceae and is different from any other known bacteria, with sequence similarities of less than 93?%. Based on phenotypic and phylogenetic findings, the isolate is considered to represent a novel genus and species in the family Ectothiorhodospiraceae, and the name Thiogranum longum gen. nov., sp. nov. is proposed. The type strain is gps52(T) (?=?NBRC 101260(T)?=?DSM 19610(T)). An emended description of the genus Thiohalomonas is also proposed. PMID:25336721

  15. Description of Colponema vietnamica sp.n. and Acavomonas peruviana n. gen. n. sp., two new alveolate phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and their contributions to reconstructing the ancestral state of alveolates and eukaryotes.

    PubMed

    Tikhonenkov, Denis V; Janouškovec, Jan; Mylnikov, Alexander P; Mikhailov, Kirill V; Simdyanov, Timur G; Aleoshin, Vladimir V; Keeling, Patrick J

    2014-01-01

    The evolutionary and ecological importance of predatory flagellates are too often overlooked. This is not only a gap in our understanding of microbial diversity, but also impacts how we interpret their better-studied relatives. A prime example of these problems is found in the alveolates. All well-studied species belong to three large clades (apicomplexans, dinoflagellates, and ciliates), but the predatory colponemid flagellates are also alveolates that are rare in nature and seldom cultured, but potentially important to our understanding of alveolate evolution. Recently we reported the first cultivation and molecular analysis of several colponemid-like organisms representing two novel clades in molecular trees. Here we provide ultrastructural analysis and formal species descriptions for both new species, Colponema vietnamica n. sp. and Acavomonas peruviana n. gen. n. sp. Morphological and feeding characteristics concur with molecular data that both species are distinct members of alveolates, with Acavomonas lacking the longitudinal phagocytotic groove, a defining feature of Colponema. Based on ultrastructure and molecular phylogenies, which both provide concrete rationale for a taxonomic reclassification of Alveolata, we establish the new phyla Colponemidia nom. nov. for the genus Colponema and its close relatives, and Acavomonidia nom. nov. for the genus Acavomonas and its close relatives. The morphological data presented here suggests that colponemids are central to our understanding of early alveolate evolution, and suggest they also retain features of the common ancestor of all eukaryotes. PMID:24740116

  16. Description of Colponema vietnamica sp.n. and Acavomonas peruviana n. gen. n. sp., Two New Alveolate Phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and Their Contributions to Reconstructing the Ancestral State of Alveolates and Eukaryotes

    PubMed Central

    Tikhonenkov, Denis V.; Janouškovec, Jan; Mylnikov, Alexander P.; Mikhailov, Kirill V.; Simdyanov, Timur G.; Aleoshin, Vladimir V.; Keeling, Patrick J.

    2014-01-01

    The evolutionary and ecological importance of predatory flagellates are too often overlooked. This is not only a gap in our understanding of microbial diversity, but also impacts how we interpret their better-studied relatives. A prime example of these problems is found in the alveolates. All well-studied species belong to three large clades (apicomplexans, dinoflagellates, and ciliates), but the predatory colponemid flagellates are also alveolates that are rare in nature and seldom cultured, but potentially important to our understanding of alveolate evolution. Recently we reported the first cultivation and molecular analysis of several colponemid-like organisms representing two novel clades in molecular trees. Here we provide ultrastructural analysis and formal species descriptions for both new species, Colponema vietnamica n. sp. and Acavomonas peruviana n. gen. n. sp. Morphological and feeding characteristics concur with molecular data that both species are distinct members of alveolates, with Acavomonas lacking the longitudinal phagocytotic groove, a defining feature of Colponema. Based on ultrastructure and molecular phylogenies, which both provide concrete rationale for a taxonomic reclassification of Alveolata, we establish the new phyla Colponemidia nom. nov. for the genus Colponema and its close relatives, and Acavomonidia nom. nov. for the genus Acavomonas and its close relatives. The morphological data presented here suggests that colponemids are central to our understanding of early alveolate evolution, and suggest they also retain features of the common ancestor of all eukaryotes. PMID:24740116

  17. Discovery of a diverse clade of gregarine apicomplexans (Apicomplexa: Eugregarinorida) from Pacific eunicid and onuphid polychaetes, including descriptions of Paralecudina n. gen., Trichotokara japonica n. sp., and T. eunicae n. sp.

    PubMed

    Rueckert, Sonja; Wakeman, Kevin C; Leander, Brian S

    2013-01-01

    Marine gregarines are poorly understood apicomplexan parasites with large trophozoites that inhabit the body cavities of marine invertebrates. Two novel species of gregarines were discovered in polychaete hosts collected in Canada and Japan. The trophozoites of Trichotokara japonica n. sp. were oval to rhomboidal shaped, and covered with longitudinal epicytic folds with a density of six to eight folds/micron. The nucleus was situated in the middle of the cell, and the mucron was elongated and covered with hair-like projections; antler-like projections also extended from the anterior tip of the mucron. The distinctively large trophozoites of Trichotokara eunicae n. sp. lacked an elongated mucron and had a tadpole-like cell shape consisting of a bulbous anterior region and a tapered tail-like posterior region. The cell surface was covered with longitudinal epicytic folds with a density of three to five folds/micron. Small subunit (SSU) rDNA sequences of both species were very divergent and formed a strongly supported clade with the recently described species Trichotokara nothriae and an environmental sequence (AB275074). This phylogenetic context combined with the morphological features of T. eunicae n. sp. required us to amend the description for Trichotokara. The sister clade to the Trichotokara clade consisted of environmental sequences and Lecudina polymorpha, which also possesses densely packed epicyctic folds (3-5 folds/micron) and a prominently elongated mucron. This improved morphological and molecular phylogenetic context justified the establishment of Paralecudina (ex. Lecudina) polymorpha n. gen. et comb. PMID:23347320

  18. Gryllotalpicola gen. nov., with descriptions of Gryllotalpicola koreensis sp. nov., Gryllotalpicola daejeonensis sp. nov. and Gryllotalpicola kribbensis sp. nov. from the gut of the African mole cricket, Gryllotalpa africana, and reclassification of Curtobacterium ginsengisoli as Gryllotalpicola ginsengisoli comb. nov.

    PubMed

    Kim, Hyangmi; Park, Doo-Sang; Oh, Hyun-Woo; Lee, Kang Hyun; Chung, Dong-Ho; Park, Ho-Yong; Park, Hee-Moon; Bae, Kyung Sook

    2012-10-01

    Strains RU-16(T), RU-28, RU-04(T) and PU-02(T) were isolated from the gut of the African mole cricket, Gryllotalpa africana. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains belonged to the family Microbacteriaceae. All four strains were most closely related to Curtobacterium ginsengisoli DCY26(T) (below 97% 16S rRNA gene sequence similarity). These isolates were Gram-stain-positive, motile (by gliding), rod-shaped and exhibited ivory-coloured colonies. Their chemotaxonomic properties included MK-11 as the major respiratory quinone, ornithine as the cell-wall diamino acid, acetyl as the acyl type of the peptidoglycan, cyclohexyl-C(17:0) as the major fatty acid and phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, we propose a new genus in the family Microbacteriaceae, Gryllotalpicola gen. nov., with three novel species, Gryllotalpicola daejeonensis sp. nov. (type strain RU-04(T) ?=KCTC 13809(T) ?=JCM 17590(T)), Gryllotalpicola koreensis sp. nov. (type strain RU-16(T) ?=?KCTC 13810(T) ?=JCM 17591(T)) and Gryllotalpicola kribbensis sp. nov. (type strain PU-02(T) ?=KCTC 13808(T) ?=JCM 17593(T)). Gryllotalpicola koreensis is the type species of the genus. Additionally, we propose that Curtobacterium ginsengisoli should be reclassified in the genus as Gryllotalpicola ginsengisoli comb. nov. (type strain DCY26(T) ?=KCTC 13163(T) ?=?JCM 14773(T)). PMID:22140167

  19. Revision of the East Mediterranean Orthomus (Coleoptera, Carabidae, Pterostichini), with description of Parorthomus gen. n. socotranus sp. n. from Socotra Island and key to the Old World genera of subtribe Euchroina.

    PubMed

    Guéorguiev, Borislav; Wrase, David W; Farka?, Jan

    2014-01-01

    The East Mediterranean species of Orthomus Chaudoir, 1838 are revised. The type series of Feronia longula Reiche & Saulcy, 1855, F. berytensis Reiche & Saulcy, 1855, F. proelonga Reiche & Saulcy, 1855, Orthomus longior Chaudoir, 1873, O. sidonicus Chaudoir, 1873, and O. berytensis akbensis Mateu, 1955 were studied and lectotypes for the first four are designated. Also, the following nomenclatural acts are proposed: Feronia proelonga Reiche & Saulcy, 1855, syn. n. of Orthomus berytensis (Reiche & Saulcy, 1855); Feronia elongata Chaudoir, 1859, syn. n. of Orthomus berytensis (Reiche & Saulcy, 1855); Orthomus sidonicus Chaudoir, 1873, syn. n. of Orthomus longior Chaudoir, 1873; Orthomus velocissimus andalusiacus Mateu, 1957, syn. n. of Orthomus velocissimus akbensis Mateu, 1955, new assignment for Orthomus berytensis akbensis Mateu, 1955. As a result, three species of the genus inhabit the East Mediterranean biogeographical region: O. berytensis, O. longior, and O. longulus. A key to these three species is given. O. longior is recorded for Turkey and Syria for the first time. In addition, a new synonymy of two West Mediterranean taxa is proposed: O. szekessyi (Jedli?ka, 1956), syn. n. of O. balearicus (Piochard de la Brûlerie, 1868), and a new genus and a species are described: Parorthomus gen. n. socotranus sp. n. (type locality: Republic of Yemen, Socotra Archipelago, Socotra Island, Fimihin env., 530 m.a.s.l.). Illustrations of the species dealt with here are provided including external characters, habitus, mentum and submentum, and genitalia are provided. Nine genera of the "African Series" of subtribe Euchroina Chaudoir, 1874 are keyed for the first time. Checklists of the species of Orthomus and of the Old World euchroine genera are given. PMID:25147463

  20. Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae.

    PubMed

    Lin, Yi-Chueh; Uemori, Kazunori; de Briel, Dominique A; Arunpairojana, Vallapa; Yokota, Akira

    2004-09-01

    Seven strains of actinobacteria, isolated from soil, wounds, urine, cow faeces, human blood and butter, were characterized by a polyphasic approach to clarify their taxonomic position. On the basis of chemotaxonomy, 16S rRNA gene analysis and DNA relatedness, strain IAM 14851T can be classified within the cluster of the genus Leucobacter and is proposed as a novel species, Leucobacter albus sp. nov., with strain IAM 14851T (=TISTR 1515T) as the type strain. The other six strains formed a phylogenetically separate branch in the family Microbacteriaceae, having the following characteristics: the major menaquinones are MK-8 to MK-10, the DNA G + C content ranges from 62 to 68 mol%, the diamino acid in the cell wall is diaminobutyric acid and the muramic acid in the peptidoglycan is of the acetyl type. The major fatty acids are 12-methyltetradecanoic acid (anteiso-C(15 : 0)), hexadecanoic acid (C(16 : 0)), 14-methyl-pentadecanoic acid (iso-C(16 : 0)) and 14-methyl-hexadecanoic acid (anteiso-C(17 : 0)). On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA-DNA hybridization and 16S rRNA gene sequence comparison, the novel genus Zimmermannella gen. nov. is proposed for these six strains. Four novel species are proposed: Zimmermannella helvola sp. nov. (type species; type strain IAM 14726T = NBRC 15775T = DSM 20419T = TISTR 1509T), Zimmermannella alba sp. nov. (type strain IAM 14724T = NBRC 15616T = TISTR 1510T), Zimmermannella bifida sp. nov. (type strain IAM 14848T = TISTR 1511T) and Zimmermannella faecalis sp. nov. (type strain IAM 15030T = NBRC 15706T = ATCC 13722T = TISTR 1514T). PMID:15388726

  1. Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria.

    PubMed

    Yabe, Shuhei; Aiba, Yoshifumi; Sakai, Yasuteru; Hazaka, Masaru; Yokota, Akira

    2011-04-01

    Two thermophilic, Gram-stain-positive, sporulating bacterial strains, which formed branched vegetative and aerial mycelia, were isolated from fallen leaves sampled from geothermal soils and designated ONI-1(T) and ONI-5(T). Strain ONI-1(T) grew at 50-74 °C, with optimum growth at 60-65 °C, and strain ONI-5(T) grew at 45-74 °C, with optimum growth at 60-65 °C. The pH range for growth of the strains was pH 4.6-8.0, with optimum growth at pH 7.0. The DNA G+C contents of strains ONI-1(T) and ONI-5(T) were 60.2 and 58.1 mol%, respectively. The major fatty acid was iso-C(17?:?0) and the major menaquinone was MK-9(H(2)). The cell walls of the strains contained glutamic acid, serine, glycine, histidine, alanine and ornithine. The polar lipids consisted of phosphatidylinositol, phosphatidylglycerol and a glycolipid. The cell-wall sugar was rhamnose. Detailed phylogenetic analysis based on 16S rRNA gene sequences indicated that the strains belong to the class Ktedonobacteria and that strains ONI-1(T) and ONI-5(T) are most closely related to Thermosporothrix hazakensis SK20-1(T) (85.3 and 84.5?% sequence similarity, respectively). 16S rRNA gene sequence similarity between the two strains was 96.6?%. Based on the phenotypic features and phylogenetic position, we propose that strains ONI-1(T) and ONI-5(T) constitute a novel genus containing two novel species, for which we propose the names Thermogemmatispora onikobensis gen. nov., sp. nov. (the type species; type strain ONI-1(T) ?=?JCM 16817(T) ?=?KCTC 19768(T)) and Thermogemmatispora foliorum sp. nov. (type strain ONI-5(T) ?=?JCM 16818(T) ?=?KCTC 19767(T)), within the new family Thermogemmatisporaceae fam. nov. and order Thermogemmatisporales ord. nov. PMID:20495028

  2. Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium.

    PubMed

    Yoon, J H; Kang, S S; Lee, K C; Lee, E S; Kho, Y H; Kang, K H; Park, Y H

    2001-07-01

    A bacterial strain, JG07T, isolated from the Korean traditional fermented seafood jeotgal, was subjected to a polyphasic taxonomic study. Cells of strain JG07T are cocci or short rods in the early growth phase but change to rods as the cultures age. The peptidoglycan type is A4alpha, based on L-Lys-D-Glu. The menaquinone profile is characterized by the predominance of MK-8 followed by MK-7 and MK-6. The cellular fatty acid profile contains major amounts of saturated, unsaturated and branched fatty acids. The cellular phospholipids are phosphatidylethanolamine, phosphatidylglycerol and bisphosphatidylglycerol. The G+C content of the DNA is 47 mol%. Phylogenetic analysis showed that strain JG07T forms a cluster with Planococcus okeanokoites and Planococcus mcmeekinii, and the relationship between this cluster and two other Planococcus species described previously is supported by bootstrap analysis at a confidence level of 100%. The 16S-23S internally transcribed spacer (ITS) sequence similarity and DNA-DNA relatedness values between strain JG07T and the type strains of other Planococcus species are in the range 74.6-83.2% and 10.4-20.5%, respectively. On the basis of the phenotypic and phylogenetic data and the genomic distinctiveness, strain JG07T is considered to represent a new genus and a new species, for which the name Planomicrobium koreense gen. nov., sp. nov. is proposed. It is also proposed that Planococcus okeanokoites and Planococcus mcmeekinii be transferred to the new genus Planomicrobium as Planomicrobium okeanokoites and Planomicrobium mcmeekinii, respectively. PMID:11491353

  3. Diversity of grass-associated Microbacteriaceae isolated from the phyllosphere and litter layer after mulching the sward; polyphasic characterization of Subtercola pratensis sp. nov., Curtobacterium herbarum sp. nov. and Plantibacter flavus gen. nov., sp. nov.

    PubMed

    Behrendt, Undine; Ulrich, Andreas; Schumann, Peter; Naumann, Dieter; Suzuki, Ken-ichiro

    2002-09-01

    A representative selection of coryneform bacteria, isolated from the phyllosphere of grasses and the litter layer after mulching the sward, was characterized by a polyphasic approach to clarify their taxonomic position in the family Microbacteriaceae, with particular reference to potentially plant-pathogenic bacteria. On the basis of 16S rDNA analysis, the isolates can be classified into six genotypes representing the genera Curtobacterium, Clavibacter, Subtercola and a subgroup, which was not affiliated to a known genus. One genotype, belonging to the genus Curtobacterium, had an identical 16S rDNA sequence to reference strains of the Curtobacterium flaccumfaciens pathovars. Another genotype, closely related to the potentially pathogenic Curtobacterium flaccumfaciens, could be distinguished from known species of the genus on the basis of phylogenetic and phenotypic characterization and is consequently proposed as a novel species, Curtobacterium herbarum sp. nov. (type strain P 420/07T DSM 14013T = LMG 19917T). Two genotypes assigned to Clavibacter showed a close relationship to Clavibacter michiganensis subsp. tessellarius, a pathogenic bacterium causing foliar lesions on wheat. A further genotype, which clustered clearly in the genus Subtercola by comparison of 16S rDNA sequences, showed a hitherto undescribed B-type of peptidoglycan containing the diagnostic diamino acids ornithine and 2,4-diaminobutyric acid, in the cell wall; this genotype is proposed as Subtercola pratensis sp. nov. (type strain P 229/10T = DSM 14246T = LMG 21000T). For one genotype, which formed a phylogenetically separate branch in the family of Microbacteriaceae showing chemotaxonomic similarities to the genus Rathayibacter, a novel genus, Plantibacter gen. nov., is proposed; the type species is Plantibacter flavus sp. nov. (type strain P 297/02T = DSM 14012T = LMG 19919T). PMID:12361245

  4. Enteractinococcus coprophilus gen. nov., sp. nov., of the family Micrococcaceae, isolated from Panthera tigris amoyensis faeces, and transfer of Yaniella fodinae Dhanjal et al. 2011 to the genus Enteractinococcus as Enteractinococcus fodinae comb. nov.

    PubMed

    Cao, Yan-Ru; Jiang, Yi; Jin, Rong-Xian; Han, Li; He, Wen-Xiang; Li, You-Long; Huang, Xue-Shi; Xue, Quan-Hong

    2012-11-01

    A novel actinobacterium, designated strain YIM 100590(T), was isolated from Panthera tigris amoyensis faeces collected from Yunnan Wild Animal Park in Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain YIM 100590(T) is a member of the family Micrococcaceae. Cells were coccoid to oval (0.7-1.5 µm in diameter) occurring singly or in clusters. Growth was observed at 10-37 °C (optimum 28 °C) and at pH 7.0-11.0 (optimum pH 8.0). The major fatty acids were iso-C(15:0) (32.22%), anteiso-C(15:0) (31.64%) and iso-C(16:0) (17.38%). The peptidoglycan was of A4? type (L-Lys-Gly-L-Glu). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, dimannosyl diacylglycerol, an unknown glycolipid and two unknown phospholipids. The quinone system comprised menaquinones MK-7 (91.9%) and MK-8 (8.3%). The DNA G+C content of strain YIM 100590(T) was 56.2 mol%. Chemotaxonomic data indicated that the strain belongs to the family Micrococcaceae. On the basis of morphological and chemotaxonomic data and phylogenetic analysis, strain YIM 100590(T) is considered to represent a novel species of a new genus within the family Micrococcaceae, for which the name Enteractinococcus coprophilus gen. nov., sp. nov. is proposed. The type strain of Enteractinococcus coprophilus is YIM 100590(T) (=DSM 24083(T)=JCM 17352(T)). Yaniella fodinae DSM 22966(T) was transferred to the new genus as Enteractinococcus fodinae comb. nov. (type strain G5(T)=DSM 22966(T)=JCM 17931(T)=MTCC 9846(T)). PMID:22228667

  5. Revision of the East Mediterranean Orthomus (Coleoptera, Carabidae, Pterostichini), with description of Parorthomus gen. n. socotranus sp. n. from Socotra Island and key to the Old World genera of subtribe Euchroina

    PubMed Central

    Guéorguiev, Borislav; Wrase, David W.; Farka?, Jan

    2014-01-01

    Abstract The East Mediterranean species of Orthomus Chaudoir, 1838 are revised. The type series of Feronia longula Reiche & Saulcy, 1855, F. berytensis Reiche & Saulcy, 1855, F. proelonga Reiche & Saulcy, 1855, Orthomus longior Chaudoir, 1873, O. sidonicus Chaudoir, 1873, and O. berytensis akbensis Mateu, 1955 were studied and lectotypes for the first four are designated. Also, the following nomenclatural acts are proposed: Feronia proelonga Reiche & Saulcy, 1855, syn. n. of Orthomus berytensis (Reiche & Saulcy, 1855); Feronia elongata Chaudoir, 1859, syn. n. of Orthomus berytensis (Reiche & Saulcy, 1855); Orthomus sidonicus Chaudoir, 1873, syn. n. of Orthomus longior Chaudoir, 1873; Orthomus velocissimus andalusiacus Mateu, 1957, syn. n. of Orthomus velocissimus akbensis Mateu, 1955, new assignment for Orthomus berytensis akbensis Mateu, 1955. As a result, three species of the genus inhabit the East Mediterranean biogeographical region: O. berytensis, O. longior, and O. longulus. A key to these three species is given. O. longior is recorded for Turkey and Syria for the first time. In addition, a new synonymy of two West Mediterranean taxa is proposed: O. szekessyi (Jedli?ka, 1956), syn. n. of O. balearicus (Piochard de la Brûlerie, 1868), and a new genus and a species are described: Parorthomus gen. n. socotranus sp. n. (type locality: Republic of Yemen, Socotra Archipelago, Socotra Island, Fimihin env., 530 m.a.s.l.). Illustrations of the species dealt with here are provided including external characters, habitus, mentum and submentum, and genitalia are provided. Nine genera of the “African Series” of subtribe Euchroina Chaudoir, 1874 are keyed for the first time. Checklists of the species of Orthomus and of the Old World euchroine genera are given. PMID:25147463

  6. Cladistic assessment of subtribal affinities within the tribe Moriomorphini with description of Rossjoycea glacialis, gen. n. and sp. n. from the South Island, and revision of Meonochilus Liebherr and Marris from the North Island, New Zealand (Coleoptera, Carabidae)

    PubMed Central

    Liebherr, James K.

    2011-01-01

    Abstract Phylogenetic relationships within the tribe Moriomorphini Sloane, 1890 are analyzed cladistically based on 75 morphological characters and 21 ingroup terminal taxa rooted at a Trechus obtusus Erichson outgroup. Based on the resultant cladistic relationships, two subtribes–Moriomorphina and Amblytelina Blackburn, 1892–are recognized, with the following new synonymies proposed: Meonides Sloane, 1898 = Amblytelina (NEW SYNONYMY); Tropopterides Sloane, 1898 = Amblytelina (NEW SYNONYMY); Mecyclothoracitae Jeannel, 1940 = Amblytelina (NEW SYNONYMY). Monophyly of Moriomorphina is based on presence of elongate, parallel-sided and glabrous to nearly glabrous male parameres, whereas Amblytelina are defined most broadly by possession of conchoid parameres with narrowed, setose apices, subtending a clade defined by a more derived parameral configuration whereby elongate styloid parameres terminate in a whip-like apical extension. Representatives of all New Zealand moriomorphine genera are included in the analysis, with cladistic results necessitating description of Rossjoycea glacialis, gen. n. and sp. n., known from a single locality near the Franz Josef Glacier, Westland, South Island, New Zealand. Monophyly of Meonochilus Liebherr and Marris, 2009 is demonstrated, and its six species are taxonomically revised: Meonochilus amplipennis (Broun), Meonochilus eplicatus (Broun), Meonochilus placens (Broun), Meonochilus bellorum, sp. n., Meonochilus rectus, sp. n., and Meonochilus spiculatus, sp. n. Geographic restriction of Meonochilus to the North Island of New Zealand, coupled with its sister-group status to an Australian-based Amblytelus Erichson-Mecyclothorax Sharp clade reinforce the interpretation that Meonochilus was isolated in New Zealand by vicariance along the Norfolk Ridge, subsequent to New Zealand’s initial Cretaceous isolation from Tasmania and southeastern Australia via opening of the Tasman Sea. PMID:22371667

  7. Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum 'Verrucomicrobia', isolated from seawater by in situ cultivation.

    PubMed

    Yoon, Jaewoo; Yasumoto-Hirose, Mina; Matsuo, Yoshihide; Nozawa, Midori; Matsuda, Satoru; Kasai, Hiroaki; Yokota, Akira

    2007-07-01

    Five Gram-negative, white-pigmented, spherical, chemoheterotrophic bacteria were isolated from seawater from Japan and the Republic of Palau by use of an in situ cultivation technique. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the five novel isolates, 02PA-Ca-133(T), YM14-201(T), H-MN57(T), H-MN48 and MN1-156, were closely affiliated to members of subdivision 4 within the phylum 'Verrucomicrobia'. The novel isolates shared 96-100 % sequence similarity with each other and showed less than 90 % similarity with the cultivated strains of subdivision 4. DNA-DNA relatedness values between strains 02PA-Ca-133(T), YM14-201(T) and H-MN57(T) were less than 70 %; the value commonly accepted as the threshold for the phylogenetic definition of a species. Antibiotic susceptibility tests and amino acid analysis of cell-wall hydrolysates indicated that the novel isolates did not contain muramic acid or diaminopimelic acid in their cell walls, suggesting that these strains lack peptidoglycan. The DNA G+C contents of the five strains were 51-57 mol%. The major menaquinone was MK-7 and C(16 : 0), C(16 : 1)omega 7c and anteiso-C(15 : 0) were the major fatty acids. On the basis of polyphasic taxonomic evidence, it is concluded that these strains should be classified as representing a new genus and three novel species in subdivision 4 of the phylum 'Verrucomicrobia', for which the names Pelagicoccus mobilis gen. nov., sp. nov. [type strain 02PA-Ca-133(T) (=MBIC08004(T)=IAM 15422(T)=KCTC 13126(T))], Pelagicoccus albus sp. nov. [type strain YM14-201(T) (=MBIC08272(T)=IAM 15421(T)=KCTC 13124(T))] and Pelagicoccus litoralis sp. nov. [type strain H-MN57(T) (=MBIC08273(T)=IAM 15423(T)=KCTC 13125(T))] are proposed. PMID:17625161

  8. HumCanGenProj_FINAL_.doc

    Cancer.gov

    The Working Group on Biomedical Technology strongly recommends the creation of a Human Cancer Genome Project (HCGP). The project’s goal would be to obtain a comprehensive description of the genetic basis of human cancer. Specifically, the project would aim to identify and characterize all the sites of genomic alteration associated at significant frequency with all major types of cancers.

  9. Von-Hippel-Lindau-Gen-Mutationstypen

    Microsoft Academic Search

    V. D. Luu; B. Fischer; A. von Teichman; G. Boysen; K. Mertz; P. Zimmermann; H. Moch; P. Schraml

    2008-01-01

    Zusammenfassung\\u000a Fragestellung  Der Von-Hippel-Lindau- (VHL-)Tumorsuppressor ist ein multifunktionelles Protein. VHL-Mutationen treten häufig auf im klarzelligen Nierenzellkarzinom (kNZK). Verschiedene Mutationstypen führen vermutlich zu\\u000a spezifischen pVHL-Funktionsveränderungen, die wiederum einen signifikanten Einfluss auf die Genexpression und schließlich\\u000a auf den Krankheitsverlauf haben dürften. Ziel der vorliegenden Studie ist die Korrelation von Genexpressionssignaturen mit\\u000a spezifischen VHL-Mutationstypen im kNZK.\\u000a \\u000a \\u000a \\u000a Methodik  Transkriptomanalyse wurde für 94 kNZK und 21 papilläre

  10. DefinitionCode Gen Ed Code Definitions

    E-print Network

    Massachusetts at Amherst, University of

    Survey Of Afro-American Lit AL AFROAM 151 Literature & Culture AL AFROAM 234 Lit. Harlem Renaissance AL COMP-LIT 319 Representing the Holocaust AL ENGLISH 115 American Experience AL ENGLISH 115H American Experience AL ENGLISH 116 Native American Literature AL ENGLISH 117 Ethnic American Literature AL ENGLISH 131

  11. questions on specific awards. However, in gen-

    E-print Network

    Myers, Lawrence C.

    accelerat- ing spending on any re- maining dollars on awards made under the American Recovery and Reinvest of these awards were received from the National Science Foun- dation and the National Institutes of Health. Over with Dartmouth's cognizant audit agency, DHHS for a new facilities and administrative cost rate. The new rates

  12. GenCade Applications Ashley Frey

    E-print Network

    US Army Corps of Engineers

    fill volumes Used yearly maintenance dredging records and split volumes into East and West bypassing effect on shoreline position, with little difference between the full length and shortened groins II Secondary - East Grid Setup Beaufort Inlet 1997 initial shoal volume estimated by subtracting yearly shoal

  13. Training Next-Gen Data Superheroes

    ERIC Educational Resources Information Center

    Waters, John K.

    2013-01-01

    The latest data alert: By 2020, the amount of data generated daily will reach 40 zettabytes, or roughly 5,247 gigabytes for every person on earth. That's one of the findings in a new report published by IT industry analysts at IDC. The study casts doubt on the ability to capture the value of all this data, especially since schools barely tapped…

  14. NexGen Production – Sequencing and Analysis

    SciTech Connect

    Muzny, Donna [Baylor College of Medicine Human Genome Sequencing Center

    2010-06-02

    Donna Muzny of the Baylor College of Medicine Human Genome Sequencing Center discusses next generation sequencing platforms and evaluating pipeline performance on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  15. Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov.

    PubMed

    Amoozegar, Mohammad Ali; Bagheri, Maryam; Didari, Maryam; Mehrshad, Maliheh; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2014-11-01

    A novel Gram-stain-positive, moderately halophilic bacterium, designated strain B6B(T), was isolated from the water of an Iranian hypersaline lake, Aran-Bidgol, and characterized taxonomically using a polyphasic approach. Cells of strain B6B(T) were rod-shaped, motile and produced ellipsoidal endospores in terminal positions in non-swollen sporangia. Strain B6B(T) was a strictly aerobic bacterium and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-20.0% (w/v), with optimum growth occurring at 10.0% (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain B6B(T) was shown to belong to the phylum Firmicutes and its closest phylogenetic similarities were with the species Virgibacillus koreensis BH30097(T) (97.5%), Virgibacillus albus YIM 93624(T) (97.4%), Sediminibacillus halophilus EN8d(T) (96.8%), Sediminibacillus albus NHBX5(T) (96.6%), Virgibacillus carmonensis LMG 20964(T) (96.3%) and Paraliobacillus quinghaiensis YIM-C158(T) (96.0%), respectively. Phylogenetic analysis revealed that strain B6B(T), along with V. koreensis BH30097(T) and V. albus YIM 93624(T), clustered in a separate clade in the family Bacillaceae. The DNA G+C content of the novel isolate was 35.8 mol%. DNA-DNA hybridization experiments revealed low levels of relatedness between strain B6B(T)and V. koreensis BH30097(T) (13%) and V. albus YIM 93624(T) (33%). The major cellular fatty acid of strain B6B(T) was anteiso-C15 : 0 (75.1%) and its polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown glycolipid. The isoprenoid quinones were MK-7 (90%) and MK-6 (3%). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All of these features support the placement of isolate B6B(T) within the phylum Firmicutes. It is closely related to V. koreensis and V. albus, but with features that clearly distinguish it from species of the genus Virgibacillus or of other related genera. On the basis of the polyphasic evidence derived in this study, we propose that strain B6B(T) be placed within a new genus, as Aquibacillus halophilus gen. nov., sp. nov., with B6B(T) as the type strain (?=IBRC-M 10775(T)?=KCTC 13828(T)). We also propose that V. koreensis and V. albus should be transferred to this new genus and be named Aquibacillus koreensis comb. nov. and Aquibacillus albus comb. nov., respectively. The type strain of Aquibacillus koreensis comb. nov. is BH30097(T) (?=KCTC 3823(T)?=IBRC-M 10657(T)?=JCM 12387(T)) and the type strain of Aquibacillus albus comb. nov. is YIM 93624(T) (?=DSM 23711(T)?=IBRC-M 10798(T)?=JCM 17364(T)). PMID:25062698

  16. Psychrobacillus gen. nov. and proposal for reclassification of Bacillus insolitus Larkin & Stokes, 1967, B. psychrotolerans Abd-El Rahman et al., 2002 and B. psychrodurans Abd-El Rahman et al., 2002 as Psychrobacillus insolitus comb. nov., Psychrobacillus psychrotolerans comb. nov. and Psychrobacillus psychrodurans comb. nov.

    PubMed

    Krishnamurthi, S; Ruckmani, A; Pukall, R; Chakrabarti, T

    2010-11-01

    The taxonomic status of three Bacillus species, Bacillus insolitus, B. psychrodurans and B. psychrotolerans was reexamined using a polyphasic approach. In our analysis, these three Bacillus species formed a cluster separate from other members of Bacillus rRNA group 2 [5] and from Bacillus sensu stricto. These three species shared high 16S rRNA gene sequence similarities between them (97.8-99.7%) and showed closest sequence similarity (95.3-96.3%) to Paenisporosarcina quisquiliarum gen. nov., sp. nov. [18]. Sequence similarities with other related genera ranged between 90.9% and 94.5%. Phylogenetic coherence of the three species was supported by phenotypic characteristics, such as growth at low temperatures, negative oxidation and assimilation of many carbohydrates, MK8 as the major isoprenoid quinine and broadly similar polar lipid profiles. All three species had a similar peptidoglycan type of the variation A4? and similar genomic G+C contents (35.7-36.6 mol% [1]). Genomic relatedness among them was shown to be less than 70% and justified their separate species status [1]. These three species could be differentiated from each other and from related taxa on the basis of phenotypic, including chemotaxonomic, characteristics and ribotype patterns. On the basis of our analysis, we propose a new genus Psychrobacillus gen. nov. and to transfer B. insolitus, B. psychrodurans and B. psychrotolerans to the new genus as Psychrobacillus insolitus comb. nov. (type species of the genus; type strain W16B(T)=DSM 5(T)), P. psychrodurans comb. nov. (type strain 68E3(T)=DSM 11713(T)) and P. psychrotolerans comb. nov. (type strain 3H1(T)=DSM 11706(T)). PMID:20650590

  17. Gen 677 Web Project Gen 677 Semester Long Project Spring 2013

    E-print Network

    Skop, Ahna

    /protein for which they have found a mutation. OMIM (Online Mendelian Inheritance in Man): http://www.ncbi.nlm.nih.gov and disease/trait. (search on PubMed for article) http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed · You

  18. Gen 677 Web Project Gen 677 Semester Long Project Spring 2012

    E-print Network

    Skop, Ahna

    /protein for which they have found a mutation. Genes and Disease: http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/gnd/tocstatic.html OMIM (Online Mendelian Inheritance in Man): http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim · You/trait. (search on PubMed for article) http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed · You will present your

  19. Hanstruepera neustonica gen. nov., sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from estuarine water, and emendation of Sediminibacter furfurosus Khan et al. 2007 emend. Kwon et al. 2014, Mangrovimonas yunxiaonensis Li et al. 2013, Antarcticimonas flava Yang et al. 2009 and Hoppeia youngheungensis Kwon et al. 2014.

    PubMed

    Hameed, Asif; Shahina, Mariyam; Lai, Wei-An; Lin, Shih-Yao; Liu, You-Cheng; Hsu, Yi-Han; Young, Chiu-Chung

    2015-02-01

    A Gram-staining-negative, strictly aerobic, yellowish-orange, flexirubin-positive, rod-shaped, non-flagellated, non-spore-forming and non-gliding marine bacterium, designated strain CC-PY-50(T), was isolated from estuarine water off Pingtung, Taiwan. The strain produced zeaxanthin as a major carotenoid pigment, and showed highest pairwise 16S rRNA gene sequence similarity to Bizionia hallyeonensis T-y7(T) (93.9 %) followed by Corallibacter vietnamensis KMM 6217(T) (93.8 %), Geojedonia litorea YCS-16(T) (93.7 %) and other members of the family Flavobacteriaceae (<93.7 %). Strain CC-PY-50(T) established a distinct phyletic lineage associated with Mangrovimonas yunxiaonensis LYYY01(T) (93.1 % sequence similarity) with poor bootstrap support during neighbour-joining and maximum-likelihood phylogenetic analyses (37 % for each). The polar lipid profile of strain CC-PY-50(T) was determined to accommodate large numbers of unknown lipids including major amounts of three unidentified aminolipids and two unidentified lipids, and moderate amounts of an unidentified phospholipid, an unidentified glycolipid and an unidentified lipid. In addition, phosphatidylethanolamine was also detected in significant amounts. The major (>5 % of total) fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, C16 : 0 and C16 : 1?6c and/or C16 : 1?7c. The DNA G+C content was 37.1 mol% and menaquinone-6 (MK-6) was the sole respiratory quinone. Based on the phylogenetic evidence and several distinguishing phenotypic and chemotaxonomic features, strain CC-PY-50(T) is proposed to represent a novel genus and species of the family Flavobacteriaceae, for which the name Hanstruepera neustonica gen. nov., sp. nov. is proposed. The type strain of the type species Hanstruepera neustonica gen. nov., sp. nov. is CC-PY-50(T) (?= JCM 19743(T)?= BCRC 80747(T)). Emended descriptions of the species Sediminibacter furfurosus, Mangrovimonas yunxiaonensis, Antarcticimonas flava and Hoppeia youngheungensis are also proposed. PMID:25351879

  20. Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th.

    PubMed

    Nazina, T N; Tourova, T P; Poltaraus, A B; Novikova, E V; Grigoryan, A A; Ivanova, A E; Lysenko, A M; Petrunyaka, V V; Osipov, G A; Belyaev, S S; Ivanov, M V

    2001-03-01

    Five hydrocarbon-oxidizing strains were isolated from formation waters of oilfields in Russia, Kazakhstan and China. These strains were moderately thermophilic, neutrophilic, motile, spore-forming rods, aerobic or facultatively anaerobic. The G+C content of their DNA ranged from 49.7 to 52.3 mol%. The major isoprenoid quinone was menaquinone-7; cellular fatty acid profiles consisted of significant amounts of iso-15:0, iso-16:0 and iso-17:0 fatty acids (61.7-86.8% of the total). Based on data from 16S rDNA analysis and DNA-DNA hybridization, the subsurface isolates could be divided into two groups, one of which consisted of strains UT and X and the other of which consisted of strains K, Sam and 34T. The new strains exhibited a close phylogenetic relationship to thermophilic bacilli of 'Group 5' of Ash et al. [Ash, C., Farrow, J. A. E., Wallbanks, S. & Collins, M. D. (1991). Lett Appl Microbiol 13, 202-206] and a set of corresponding signature positions of 16S rRNA. Comparative analysis of the 16S rDNA sequences and fatty acid compositions of the novel isolates and established species of thermophilic bacilli indicated that the subsurface strains represent two new species within a new genus, for which the names Geobacillus subterraneus gen. nov., sp. nov., and Geobacillus uzenensis sp. nov. are proposed. It is also proposed that Bacillus stearothermophilus, Bacillus thermoleovorans, Bacillus thermocatenulatus, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans be transferred to this new genus, with Geobacillus stearothermophilus (formerly Bacillus stearothermophilus) as the type species. PMID:11321089